https:/// /w/api.php?action=feedcontributions&user=FolkerMeyer&feedformat=atomTheSeed - User contributions [en]2024-03-29T14:43:13ZUser contributionsMediaWiki 1.35.6 /w/index.php?title=Home_of_the_SEED&diff=2481Home of the SEED2009-11-23T20:03:02Z<p>FolkerMeyer: added link to FIGfam page</p>
<hr />
<div>With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. <br />
<br />
[[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]]<br />
<br />
Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([http://seed-viewer.theseed.org/seedviewer.cgi?page=FigFamViewer FIGfams]). These FIGfams form the core component of our RAST automated annotation technology.<br />
<br />
<br />
Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. <br />
<br />
We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page.<br />
<br />
* We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material])<br />
* We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material])<br />
* Our approaches to annotation, gene calling, etc. are outlined in a series of [http://www.nmpdr.org/FIG/wiki/view.cgi/SOP/WebHome| Standard Operating Procedures].<br />
* Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications#Using Publications] page.</div>FolkerMeyer /w/index.php?title=FIGfams/&diff=2480FIGfams/2009-04-27T18:13:50Z<p>FolkerMeyer: </p>
<hr />
<div>This is the new home of the FIGfams (ALEX is going to make it that)</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0&diff=1846MG RAST v2.02008-06-28T22:24:16Z<p>FolkerMeyer: /* Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) */</p>
<hr />
<div>== MG-RAST v2.0 Homepage ==<br />
<br />
=== What is MG-RAST ( Executive Summary) ===<br />
<br />
MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs.<br />
<br />
In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases.<br />
<br />
Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes.<br />
<br />
=== Overview ===<br />
<br />
The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes.<br />
<br />
The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database.<br />
<br />
User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats.<br />
<br />
To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address.<br />
<br />
<br />
=== What's new in v2.0? (Changes from MG-RAST v1.2) ===<br />
We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0:<br />
<br />
* Significant improvements of user interface responsiveness and overall performance.<br />
* The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use.<br />
* The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]).<br />
* The <strong>ability to modify parameters for sequence comparison</strong> underlying both metabolic reconstruction and phylogenetic reconstruction on the fly.<br />
* The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions.<br />
* We have added a <strong> recruitment plot </strong>feature, plotting fragments against microbial genomes.<br />
* We have added the ability to <strong> view all BLAST hits for a fragment </strong> and show the individual BLAST alignments.<br />
* The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview).<br />
* We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0<br />
* We have also <strong>updated the underlying databases</strong>. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database])<br />
* Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. <br />
* Support for user driven creation and maintenance of groups.<br />
* The ability to support arbitrary sets and versions of databases.<br />
* Many small detailed fixes and improvements.<br />
<br />
== Databases used ==<br />
* [http://www.theseed.org SEED non redundant protein database]<br />
* [http://greengenes.lbl.gov/ GREENGENES]<br />
* [http://rdp.cme.msu.edu/ RDP-II]<br />
* [http://www.arb-silva.de/ SILVA]<br />
<br />
== Standard Compliance ==<br />
We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO"<br />
<br />
== Navigating MG-RAST v2.0 ==<br />
[[Image:MG-Rast Navigation Overview.jpg]]<br />
<br />
== Manual for MG-RAST v2.0 ==<br />
Separate page<br />
== Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) ==<br />
A [[MG_RAST_v2.0_tutorial|tour]] of the user interface.<br />
<br />
== Availability==<br />
Using MG-RAST is free for all users. We provide privacy for the data submitted and <br />
<br />
MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. <br />
<br />
== Frequently asked questions (FAQ) ==<br />
<br />
We provide a list of frequently asked questions at [[MG_RAST_v2.0_FAQ]].<br />
<br />
== Contact ==<br />
Once logged in to the system, the address of the MG-RAST system will be available to all users.</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0_tutorial&diff=1845MG RAST v2.0 tutorial2008-06-27T23:45:13Z<p>FolkerMeyer: </p>
<hr />
<div>This page will contain a tutorial for version 2.0 of MG-RAST.</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0_FAQ&diff=1844MG RAST v2.0 FAQ2008-06-20T22:38:59Z<p>FolkerMeyer: </p>
<hr />
<div>=== What are projects? ===<br />
Projects are related sets of metagenomes. If you for example plan on studying a set of samples from a chronoseries, it might me useful to group them into a project.<br />
<br />
=== What level of privacy does MG-RAST v2.0 provide? ===<br />
We provide password control and the ability for the submitting entity to control access on a username/password basis to the submitted data sets.<br />
<br />
Note that we currently do not provide industry standard encryption as this would put additional load on our server infrastructure and is not strictly required for scientific purposes.<br />
<br />
=== Do you support BLASTing against my private database XYZ? ===<br />
We currently do not explicitly support this, however the underlying software design end system architecture support this. <br />
<br />
=== How frequently do you update the underlying NR for MG-RAST? ===<br />
With version 2.0 we have added the support for multiple concurrent sets of sequence similarity results to be stored per metagenome. We can add results for newer NRs. However once you start comparing results for metagenomes (say you are interested in the phylogenetic reconstruction) different versions of the NR used for the underlying data will lead to incorrect comparison results as older versions of NR will miss certain organisms and or annotations.<br />
<br />
=== How long does it take to analyze my Metagenome? ===<br />
The answer depends on two factors a) the size of your data set and b) the current server load. Under optimal conditions, it takes about 18 hours to run a 100 million basepair 454 metagenome through the pipeline.<br />
<br />
=== How many metagenomes can I submit? ===<br />
We do not restrict user submission of samples. However the computation required is massive and samples are processed on a first come first serve basis. <br />
<br />
=== What parameters should I use to analyze my data? ===<br />
The answer depends on your sample. In any case we recommend that you modify e-value, minimal alignment length and percent identity requirements for the BLAST results underlying the results. The effects of this are different for each sample. Depending on sample complexity, sample size, number of species an diversity of species present your results will vary dramatically when modifying these parameters. For RNA based phylogenetic reconstruction, we recommend requiring a minimum alignment length of 50bp for exact matches.<br />
<br />
=== Where can people access my "published" metagenomes? ===<br />
The MG-RAST v2.0 Homepage has a list of publicly accessible metagenomes. <br />
<br />
Future versions will continue to support this feature, also we will provide a metadata based selection tool, that will allow the user to focus on metagenome data sets from the environment or condition etc they are interested in.<br />
<br />
=== What about HIPAA relevant data? ===<br />
MG-RAST is provided under the assumption that all data is anonymized, no [http://en.wikipedia.org/wiki/HIPAA HIPAA] relevant data should be stored on MG-RAST.<br />
<br />
=== How can I download a subset of fragments in FASTA format? ===<br />
Many pages support downloading the data into a spreadsheet format (eg MS Excel). One the Metabolic Reconstruction page or the Phylogenetic reconstruction, you can download a subset of the fragments contained in the sample matching a specific group of organisms or matching a specific part of metabolism via clicking on the tab for Tabular view. There you click on a given subset.<br />
<br />
<br />
<br />
<br />
=== How are the numbers computed? ===<br />
<font color="red">NEEDS TO BE FILLED</font></div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0&diff=1843MG RAST v2.02008-06-20T22:30:51Z<p>FolkerMeyer: /* Navigating MG-RAST v2.0 */</p>
<hr />
<div>== MG-RAST v2.0 Homepage ==<br />
<br />
=== What is MG-RAST ( Executive Summary) ===<br />
<br />
MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs.<br />
<br />
In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases.<br />
<br />
Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes.<br />
<br />
=== Overview ===<br />
<br />
The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes.<br />
<br />
The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database.<br />
<br />
User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats.<br />
<br />
To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address.<br />
<br />
<br />
=== What's new in v2.0? (Changes from MG-RAST v1.2) ===<br />
We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0:<br />
<br />
* Significant improvements of user interface responsiveness and overall performance.<br />
* The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use.<br />
* The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]).<br />
* The <strong>ability to modify parameters for sequence comparison</strong> underlying both metabolic reconstruction and phylogenetic reconstruction on the fly.<br />
* The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions.<br />
* We have added a <strong> recruitment plot </strong>feature, plotting fragments against microbial genomes.<br />
* We have added the ability to <strong> view all BLAST hits for a fragment </strong> and show the individual BLAST alignments.<br />
* The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview).<br />
* We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0<br />
* We have also <strong>updated the underlying databases</strong>. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database])<br />
* Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. <br />
* Support for user driven creation and maintenance of groups.<br />
* The ability to support arbitrary sets and versions of databases.<br />
* Many small detailed fixes and improvements.<br />
<br />
== Databases used ==<br />
* [http://www.theseed.org SEED non redundant protein database]<br />
* [http://greengenes.lbl.gov/ GREENGENES]<br />
* [http://rdp.cme.msu.edu/ RDP-II]<br />
* [http://www.arb-silva.de/ SILVA]<br />
<br />
== Standard Compliance ==<br />
We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO"<br />
<br />
== Navigating MG-RAST v2.0 ==<br />
[[Image:MG-Rast Navigation Overview.jpg]]<br />
<br />
== Manual for MG-RAST v2.0 ==<br />
Separate page<br />
== Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) ==<br />
Separate page<br />
<br />
== Availability==<br />
Using MG-RAST is free for all users. We provide privacy for the data submitted and <br />
<br />
MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. <br />
<br />
== Frequently asked questions (FAQ) ==<br />
<br />
We provide a list of frequently asked questions at [[MG_RAST_v2.0_FAQ]].<br />
<br />
== Contact ==<br />
Once logged in to the system, the address of the MG-RAST system will be available to all users.</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0&diff=1842MG RAST v2.02008-06-20T22:30:09Z<p>FolkerMeyer: /* Navigating MG-RAST v2.0 */</p>
<hr />
<div>== MG-RAST v2.0 Homepage ==<br />
<br />
=== What is MG-RAST ( Executive Summary) ===<br />
<br />
MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs.<br />
<br />
In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases.<br />
<br />
Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes.<br />
<br />
=== Overview ===<br />
<br />
The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes.<br />
<br />
The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database.<br />
<br />
User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats.<br />
<br />
To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address.<br />
<br />
<br />
=== What's new in v2.0? (Changes from MG-RAST v1.2) ===<br />
We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0:<br />
<br />
* Significant improvements of user interface responsiveness and overall performance.<br />
* The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use.<br />
* The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]).<br />
* The <strong>ability to modify parameters for sequence comparison</strong> underlying both metabolic reconstruction and phylogenetic reconstruction on the fly.<br />
* The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions.<br />
* We have added a <strong> recruitment plot </strong>feature, plotting fragments against microbial genomes.<br />
* We have added the ability to <strong> view all BLAST hits for a fragment </strong> and show the individual BLAST alignments.<br />
* The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview).<br />
* We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0<br />
* We have also <strong>updated the underlying databases</strong>. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database])<br />
* Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. <br />
* Support for user driven creation and maintenance of groups.<br />
* The ability to support arbitrary sets and versions of databases.<br />
* Many small detailed fixes and improvements.<br />
<br />
== Databases used ==<br />
* [http://www.theseed.org SEED non redundant protein database]<br />
* [http://greengenes.lbl.gov/ GREENGENES]<br />
* [http://rdp.cme.msu.edu/ RDP-II]<br />
* [http://www.arb-silva.de/ SILVA]<br />
<br />
== Standard Compliance ==<br />
We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO"<br />
<br />
== Navigating MG-RAST v2.0 ==<br />
[this will be a simple graphical overview of the pages and their links]<br />
[Image:MG-Rast Navigation Overview.jpg]<br />
<br />
== Manual for MG-RAST v2.0 ==<br />
Separate page<br />
== Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) ==<br />
Separate page<br />
<br />
== Availability==<br />
Using MG-RAST is free for all users. We provide privacy for the data submitted and <br />
<br />
MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. <br />
<br />
== Frequently asked questions (FAQ) ==<br />
<br />
We provide a list of frequently asked questions at [[MG_RAST_v2.0_FAQ]].<br />
<br />
== Contact ==<br />
Once logged in to the system, the address of the MG-RAST system will be available to all users.</div>FolkerMeyer /w/index.php?title=File:MG-Rast_Navigation_Overview.jpg&diff=1841File:MG-Rast Navigation Overview.jpg2008-06-20T22:29:41Z<p>FolkerMeyer: </p>
<hr />
<div></div>FolkerMeyer /w/index.php?title=File:MG-Rast_Navigation_Overview.png&diff=1840File:MG-Rast Navigation Overview.png2008-06-20T22:28:11Z<p>FolkerMeyer: </p>
<hr />
<div></div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0_FAQ&diff=1839MG RAST v2.0 FAQ2008-06-20T21:07:38Z<p>FolkerMeyer: </p>
<hr />
<div>=== What are projects? ===<br />
Projects are related sets of metagenomes. If you for example plan on studying a set of samples from a chronoseries, it might me useful to group them into a project.<br />
<br />
=== What level of privacy does MG-RAST v2.0 provide? ===<br />
We provide password control and the ability for the submitting entity to control access on a username/password basis to the submitted data sets.<br />
<br />
Note that we currently do not provide industry standard encryption as this would put additional load on our server infrastructure and is not strictly required for scientific purposes.<br />
<br />
=== Do you support BLASTing against my private database XYZ? ===<br />
We currently do not explicitly support this, however the underlying software design end system architecture support this. <br />
<br />
=== How frequently do you update the underlying NR for MG-RAST? ===<br />
With version 2.0 we have added the support for multiple concurrent sets of sequence similarity results to be stored per metagenome. We can add results for newer NRs. However once you start comparing results for metagenomes (say you are interested in the phylogenetic reconstruction) different versions of the NR used for the underlying data will lead to incorrect comparison results as older versions of NR will miss certain organisms and or annotations.<br />
<br />
=== How long does it take to analyze my Metagenome? ===<br />
The answer depends on two factors a) the size of your data set and b) the current server load. Under optimal conditions, it takes about 18 hours to run a 100 million basepair 454 metagenome through the pipeline.<br />
<br />
=== How many metagenomes can I submit? ===<br />
We do not restrict user submission of samples. However the computation required is massive and samples are processed on a first come first serve basis. <br />
<br />
=== What parameters should I use to analyze my data? ===<br />
The answer depends on your sample. In any case we recommend that you modify e-value, minimal alignment length and percent identity requirements for the BLAST results underlying the results. The effects of this are different for each sample. Depending on sample complexity, sample size, number of species an diversity of species present your results will vary dramatically when modifying these parameters. For RNA based phylogenetic reconstruction, we recommend requiring a minimum alignment length of 50bp for exact matches.<br />
<br />
=== Where can people access my "published" metagenomes? ===<br />
The MG-RAST v2.0 Homepage has a list of publicly accessible metagenomes. <br />
<br />
Future versions will continue to support this feature, also we will provide a metadata based selection tool, that will allow the user to focus on metagenome data sets from the environment or condition etc they are interested in.<br />
<br />
=== What about HIPAA relevant data? ===<br />
MG-RAST is provided under the assumption that all data is anonymized, no [http://en.wikipedia.org/wiki/HIPAA HIPAA] relevant data should be stored on MG-RAST.<br />
<br />
<br />
=== How are the numbers computed? ===<br />
<font color="red">NEEDS TO BE FILLED</font></div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0&diff=1838MG RAST v2.02008-06-20T18:11:21Z<p>FolkerMeyer: /* What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) */</p>
<hr />
<div>== MG-RAST v2.0 Homepage ==<br />
<br />
=== What is MG-RAST ( Executive Summary) ===<br />
<br />
MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs.<br />
<br />
In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases.<br />
<br />
Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes.<br />
<br />
=== Overview ===<br />
<br />
The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes.<br />
<br />
The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database.<br />
<br />
User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats.<br />
<br />
To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address.<br />
<br />
<br />
=== What's new in v2.0? (Changes from MG-RAST v1.2) ===<br />
We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0:<br />
<br />
* Significant improvements of user interface responsiveness and overall performance.<br />
* The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use.<br />
* The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]).<br />
* The <strong>ability to modify parameters for sequence comparison</strong> underlying both metabolic reconstruction and phylogenetic reconstruction on the fly.<br />
* The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions.<br />
* We have added a <strong> recruitment plot </strong>feature, plotting fragments against microbial genomes.<br />
* We have added the ability to <strong> view all BLAST hits for a fragment </strong> and show the individual BLAST alignments.<br />
* The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview).<br />
* We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0<br />
* We have also <strong>updated the underlying databases</strong>. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database])<br />
* Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. <br />
* Support for user driven creation and maintenance of groups.<br />
* The ability to support arbitrary sets and versions of databases.<br />
* Many small detailed fixes and improvements.<br />
<br />
== Databases used ==<br />
* [http://www.theseed.org SEED non redundant protein database]<br />
* [http://greengenes.lbl.gov/ GREENGENES]<br />
* [http://rdp.cme.msu.edu/ RDP-II]<br />
* [http://www.arb-silva.de/ SILVA]<br />
<br />
== Standard Compliance ==<br />
We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO"<br />
<br />
== Navigating MG-RAST v2.0 ==<br />
[this will be a simple graphical overview of the pages and their links]<br />
<br />
== Manual for MG-RAST v2.0 ==<br />
Separate page<br />
== Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) ==<br />
Separate page<br />
<br />
== Availability==<br />
Using MG-RAST is free for all users. We provide privacy for the data submitted and <br />
<br />
MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. <br />
<br />
== Frequently asked questions (FAQ) ==<br />
<br />
We provide a list of frequently asked questions at [[MG_RAST_v2.0_FAQ]].<br />
<br />
== Contact ==<br />
Once logged in to the system, the address of the MG-RAST system will be available to all users.</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0_FAQ&diff=1837MG RAST v2.0 FAQ2008-06-20T17:54:15Z<p>FolkerMeyer: </p>
<hr />
<div>=== What are projects? ===<br />
Projects are related sets of metagenomes. If you for example plan on studying a set of samples from a chronoseries, it might me useful to group them into a project.<br />
<br />
=== What level of privacy does MG-RAST v2.0 provide? ===<br />
We provide password control and the ability for the submitting entity to control access on a username/password basis to the submitted data sets.<br />
<br />
Note that we currently do not provide industry standard encryption as this would put additional load on our server infrastructure and is not strictly required for scientific purposes.<br />
<br />
=== Do you support BLASTing against my private database XYZ? ===<br />
We currently do not explicitly support this, however the underlying software design end system architecture support this. <br />
<br />
=== How frequently do you update the underlying NR for MG-RAST? ===<br />
With version 2.0 we have added the support for multiple concurrent sets of sequence similarity results to be stored per metagenome. We can add results for newer NRs. However once you start comparing results for metagenomes (say you are interested in the phylogenetic reconstruction) different versions of the NR used for the underlying data will lead to incorrect comparison results as older versions of NR will miss certain organisms and or annotations.<br />
<br />
=== How long does it take to analyze my Metagenome? ===<br />
The answer depends on two factors a) the size of your data set and b) the current server load. Under optimal conditions, it takes about 18 hours to run a 100 million basepair 454 metagenome through the pipeline.<br />
<br />
=== How many metagenomes can I submit? ===<br />
We do not restrict user submission of samples. However the computation required is massive and samples are processed on a first come first serve basis. <br />
<br />
=== What parameters should I use to analyze my data? ===<br />
The answer depends on your sample. In any case we recommend that you modify e-value, minimal alignment length and percent identity requirements for the BLAST results underlying the results. The effects of this are different for each sample. Depending on sample complexity, sample size, number of species an diversity of species present your results will vary dramatically when modifying these parameters. For RNA based phylogenetic reconstruction, we recommend requiring a minimum alignment length of 50bp for exact matches.<br />
<br />
=== Where can people access my "published" metagenomes? ===<br />
The MG-RAST v2.0 Homepage has a list of publicly accessible metagenomes. <br />
<br />
Future versions will continue to support this feature, also we will provide a metadata based selection tool, that will allow the user to focus on metagenome data sets from the environment or condition etc they are interested in.<br />
<br />
=== What about HIPAA relevant data? ===<br />
MG-RAST is provided under the assumption that all data is anonymized, no [http://en.wikipedia.org/wiki/HIPAA HIPAA] relevant data should be stored on MG-RAST.</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0_FAQ&diff=1836MG RAST v2.0 FAQ2008-06-20T17:53:02Z<p>FolkerMeyer: </p>
<hr />
<div>=== What are projects? ===<br />
Projects are related sets of metagenomes. If you for example plan on studying a set of samples from a chronoseries, it might me useful to group them into a project.<br />
<br />
=== What level of privacy does MG-RAST v2.0 provide? ===<br />
We provide password control and the ability for the submitting entity to control access on a username/password basis to the submitted data sets.<br />
<br />
Note that we currently do not provide industry standard encryption as this would put additional load on our server infrastructure and is not strictly required for scientific purposes.<br />
<br />
=== Do you support BLASTing against my private database XYZ? ===<br />
We currently do not explicitly support this, however the underlying software design end system architecture support this. <br />
<br />
=== How frequently do you update the underlying NR for MG-RAST? ===<br />
With version 2.0 we have added the support for multiple concurrent sets of sequence similarity results to be stored per metagenome. We can add results for newer NRs. However once you start comparing results for metagenomes (say you are interested in the phylogenetic reconstruction) different versions of the NR used for the underlying data will lead to incorrect comparison results as older versions of NR will miss certain organisms and or annotations.<br />
<br />
=== How long does it take to analyze my Metagenome? ===<br />
The answer depends on two factors a) the size of your data set and b) the current server load. Under optimal conditions, it takes about 18 hours to run a 100 million basepair 454 metagenome through the pipeline.<br />
<br />
=== What parameters should I use to analyze my data? ===<br />
The answer depends on your sample. In any case we recommend that you modify e-value, minimal alignment length and percent identity requirements for the BLAST results underlying the results. The effects of this are different for each sample. Depending on sample complexity, sample size, number of species an diversity of species present your results will vary dramatically when modifying these parameters. For RNA based phylogenetic reconstruction, we recommend requiring a minimum alignment length of 50bp for exact matches.<br />
<br />
=== Where can people access my "published" metagenomes? ===<br />
The MG-RAST v2.0 Homepage has a list of publicly accessible metagenomes. <br />
<br />
Future versions will continue to support this feature, also we will provide a metadata based selection tool, that will allow the user to focus on metagenome data sets from the environment or condition etc they are interested in.<br />
<br />
=== What about HIPAA relevant data? ===<br />
MG-RAST is provided under the assumption that all data is anonymized, no [http://en.wikipedia.org/wiki/HIPAA HIPAA] relevant data should be stored on MG-RAST.</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0_FAQ&diff=1835MG RAST v2.0 FAQ2008-06-20T17:51:39Z<p>FolkerMeyer: /* What level of privacy does MG-RAST v2.0 provide? */</p>
<hr />
<div>=== What are projects? ===<br />
Projects are related sets of metagenomes. If you for example plan on studying a set of samples from a chronoseries, it might me useful to group them into a project.<br />
<br />
=== What level of privacy does MG-RAST v2.0 provide? ===<br />
We provide password control and the ability for the submitting entity to control access on a username/password basis to the submitted data sets.<br />
<br />
Note that we currently do not provide industry standard encryption as this would put additional load on our server infrastructure and is not strictly required for scientific purposes.<br />
<br />
=== Do you support BLASTing against my private database XYZ? ===<br />
We currently do not explicitly support this, however the underlying software design end system architecture support this. <br />
<br />
=== How frequently do you update the underlying NR for MG-RAST? ===<br />
With version 2.0 we have added the support for multiple concurrent sets of sequence similarity results to be stored per metagenome. We can add results for newer NRs. However once you start comparing results for metagenomes (say you are interested in the phylogenetic reconstruction) different versions of the NR used for the underlying data will lead to incorrect comparison results as older versions of NR will miss certain organisms and or annotations.<br />
<br />
=== How long does it take to analyze my Metagenome? ===<br />
The answer depends on two factors a) the size of your data set and b) the current server load. Under optimal conditions, it takes about 18 hours to run a 100 million basepair 454 metagenome through the pipeline.<br />
<br />
=== What parameters should I use to analyze my data? ===<br />
The answer depends on your sample. In any case we recommend that you modify e-value, minimal alignment length and percent identity requirements for the BLAST results underlying the results. The effects of this are different for each sample. Depending on sample complexity, sample size, number of species an diversity of species present your results will vary dramatically when modifying these parameters. For RNA based phylogenetic reconstruction, we recommend requiring a minimum alignment length of 50bp for exact matches.<br />
<br />
=== Where can people access my "published" metagenomes? ===<br />
The MG-RAST v2.0 Homepage has a list of publicly accessible metagenomes. <br />
<br />
Future versions will continue to support this feature, also we will provide a metadata based selection tool, that will allow the user to focus on metagenome data sets from the environment or condition etc they are interested in.</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0_FAQ&diff=1834MG RAST v2.0 FAQ2008-06-20T17:50:44Z<p>FolkerMeyer: /* Where can people access the "public" metagenomes? */</p>
<hr />
<div>=== What are projects? ===<br />
Projects are related sets of metagenomes. If you for example plan on studying a set of samples from a chronoseries, it might me useful to group them into a project.<br />
<br />
=== What level of privacy does MG-RAST v2.0 provide? ===<br />
We provide password control and the ability for the submitting entity to control access on a username/password basis to the submitted data sets.<br />
<br />
=== Do you support BLASTing against my private database XYZ? ===<br />
We currently do not explicitly support this, however the underlying software design end system architecture support this. <br />
<br />
=== How frequently do you update the underlying NR for MG-RAST? ===<br />
With version 2.0 we have added the support for multiple concurrent sets of sequence similarity results to be stored per metagenome. We can add results for newer NRs. However once you start comparing results for metagenomes (say you are interested in the phylogenetic reconstruction) different versions of the NR used for the underlying data will lead to incorrect comparison results as older versions of NR will miss certain organisms and or annotations.<br />
<br />
=== How long does it take to analyze my Metagenome? ===<br />
The answer depends on two factors a) the size of your data set and b) the current server load. Under optimal conditions, it takes about 18 hours to run a 100 million basepair 454 metagenome through the pipeline.<br />
<br />
=== What parameters should I use to analyze my data? ===<br />
The answer depends on your sample. In any case we recommend that you modify e-value, minimal alignment length and percent identity requirements for the BLAST results underlying the results. The effects of this are different for each sample. Depending on sample complexity, sample size, number of species an diversity of species present your results will vary dramatically when modifying these parameters. For RNA based phylogenetic reconstruction, we recommend requiring a minimum alignment length of 50bp for exact matches.<br />
<br />
=== Where can people access my "published" metagenomes? ===<br />
The MG-RAST v2.0 Homepage has a list of publicly accessible metagenomes. <br />
<br />
Future versions will continue to support this feature, also we will provide a metadata based selection tool, that will allow the user to focus on metagenome data sets from the environment or condition etc they are interested in.</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0_FAQ&diff=1833MG RAST v2.0 FAQ2008-06-20T17:50:23Z<p>FolkerMeyer: </p>
<hr />
<div>=== What are projects? ===<br />
Projects are related sets of metagenomes. If you for example plan on studying a set of samples from a chronoseries, it might me useful to group them into a project.<br />
<br />
=== What level of privacy does MG-RAST v2.0 provide? ===<br />
We provide password control and the ability for the submitting entity to control access on a username/password basis to the submitted data sets.<br />
<br />
=== Do you support BLASTing against my private database XYZ? ===<br />
We currently do not explicitly support this, however the underlying software design end system architecture support this. <br />
<br />
=== How frequently do you update the underlying NR for MG-RAST? ===<br />
With version 2.0 we have added the support for multiple concurrent sets of sequence similarity results to be stored per metagenome. We can add results for newer NRs. However once you start comparing results for metagenomes (say you are interested in the phylogenetic reconstruction) different versions of the NR used for the underlying data will lead to incorrect comparison results as older versions of NR will miss certain organisms and or annotations.<br />
<br />
=== How long does it take to analyze my Metagenome? ===<br />
The answer depends on two factors a) the size of your data set and b) the current server load. Under optimal conditions, it takes about 18 hours to run a 100 million basepair 454 metagenome through the pipeline.<br />
<br />
=== What parameters should I use to analyze my data? ===<br />
The answer depends on your sample. In any case we recommend that you modify e-value, minimal alignment length and percent identity requirements for the BLAST results underlying the results. The effects of this are different for each sample. Depending on sample complexity, sample size, number of species an diversity of species present your results will vary dramatically when modifying these parameters. For RNA based phylogenetic reconstruction, we recommend requiring a minimum alignment length of 50bp for exact matches.<br />
<br />
=== Where can people access the "public" metagenomes? ===<br />
The MG-RAST v2.0 Homepage has a list of publicly accessible metagenomes. Future versions will continue to support this feature, also we will provide a metadata based selection tool, that will allow the user to focus on metagenome data sets from the environment or condition etc they are interested in.</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0&diff=1832MG RAST v2.02008-06-20T17:48:30Z<p>FolkerMeyer: /* What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) */</p>
<hr />
<div>== MG-RAST v2.0 Homepage ==<br />
<br />
=== What is MG-RAST ( Executive Summary) ===<br />
<br />
MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs.<br />
<br />
In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases.<br />
<br />
Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes.<br />
<br />
=== Overview ===<br />
<br />
The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes.<br />
<br />
The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database.<br />
<br />
User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats.<br />
<br />
To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address.<br />
<br />
<br />
=== What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) ===<br />
We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0:<br />
<br />
* Significant improvements of user interface responsiveness and overall performance.<br />
* The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use.<br />
* The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]).<br />
* The <strong>ability to modify parameters for sequence comparison</strong> underlying both metabolic reconstruction and phylogenetic reconstruction on the fly.<br />
* The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions.<br />
* We have added a <strong> recruitment plot </strong>feature, plotting fragments against microbial genomes.<br />
* We have added the ability to <strong> view all BLAST hits for a fragment </strong> and show the individual BLAST alignments.<br />
* The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview).<br />
* We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0<br />
* We have also <strong>updated the underlying databases</strong>. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database])<br />
* Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. <br />
* Support for user driven creation and maintenance of groups.<br />
* The ability to support arbitrary sets and versions of databases.<br />
* Many small detailed fixes and improvements.<br />
<br />
== Databases used ==<br />
* [http://www.theseed.org SEED non redundant protein database]<br />
* [http://greengenes.lbl.gov/ GREENGENES]<br />
* [http://rdp.cme.msu.edu/ RDP-II]<br />
* [http://www.arb-silva.de/ SILVA]<br />
<br />
== Standard Compliance ==<br />
We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO"<br />
<br />
== Navigating MG-RAST v2.0 ==<br />
[this will be a simple graphical overview of the pages and their links]<br />
<br />
== Manual for MG-RAST v2.0 ==<br />
Separate page<br />
== Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) ==<br />
Separate page<br />
<br />
== Availability==<br />
Using MG-RAST is free for all users. We provide privacy for the data submitted and <br />
<br />
MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. <br />
<br />
== Frequently asked questions (FAQ) ==<br />
<br />
We provide a list of frequently asked questions at [[MG_RAST_v2.0_FAQ]].<br />
<br />
== Contact ==<br />
Once logged in to the system, the address of the MG-RAST system will be available to all users.</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0&diff=1831MG RAST v2.02008-06-20T17:48:13Z<p>FolkerMeyer: /* What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) */</p>
<hr />
<div>== MG-RAST v2.0 Homepage ==<br />
<br />
=== What is MG-RAST ( Executive Summary) ===<br />
<br />
MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs.<br />
<br />
In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases.<br />
<br />
Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes.<br />
<br />
=== Overview ===<br />
<br />
The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes.<br />
<br />
The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database.<br />
<br />
User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats.<br />
<br />
To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address.<br />
<br />
<br />
=== What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) ===<br />
We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0:<br />
<br />
* Significant improvements of user interface responsiveness and overall performance.<br />
* The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use.<br />
* The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]).<br />
* The <strong>ability to modify parameters for sequence comparison</strong> underlying both metabolic reconstruction and phylogenetic reconstruction on the fly.<br />
* The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions.<br />
* We have added a <strong> recruitment plot </strong>feature, plotting fragments against microbial genomes.<br />
* We have added the ability to <strong> view all BLAST hits for a fragment </strong> and show the individual BLAST alignments.<br />
* The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview).<br />
* We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0<br />
* We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database])<br />
* Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. <br />
* Support for user driven creation and maintenance of groups.<br />
* The ability to support arbitrary sets and versions of databases.<br />
* Many small detailed fixes and improvements.<br />
<br />
== Databases used ==<br />
* [http://www.theseed.org SEED non redundant protein database]<br />
* [http://greengenes.lbl.gov/ GREENGENES]<br />
* [http://rdp.cme.msu.edu/ RDP-II]<br />
* [http://www.arb-silva.de/ SILVA]<br />
<br />
== Standard Compliance ==<br />
We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO"<br />
<br />
== Navigating MG-RAST v2.0 ==<br />
[this will be a simple graphical overview of the pages and their links]<br />
<br />
== Manual for MG-RAST v2.0 ==<br />
Separate page<br />
== Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) ==<br />
Separate page<br />
<br />
== Availability==<br />
Using MG-RAST is free for all users. We provide privacy for the data submitted and <br />
<br />
MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. <br />
<br />
== Frequently asked questions (FAQ) ==<br />
<br />
We provide a list of frequently asked questions at [[MG_RAST_v2.0_FAQ]].<br />
<br />
== Contact ==<br />
Once logged in to the system, the address of the MG-RAST system will be available to all users.</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0_FAQ&diff=1830MG RAST v2.0 FAQ2008-06-20T17:46:27Z<p>FolkerMeyer: </p>
<hr />
<div>=== What are projects? ===<br />
Projects are related sets of metagenomes. If you for example plan on studying a set of samples from a chronoseries, it might me useful to group them into a project.<br />
<br />
=== What level of privacy does MG-RAST v2.0 provide? ===<br />
We provide password control and the ability for the submitting entity to control access on a username/password basis to the submitted data sets.<br />
<br />
=== Do you support BLASTing against my private database XYZ? ===<br />
We currently do not explicitly support this, however the underlying software design end system architecture support this. <br />
<br />
=== How frequently do you update the underlying NR for MG-RAST? ===<br />
With version 2.0 we have added the support for multiple concurrent sets of sequence similarity results to be stored per metagenome. We can add results for newer NRs. However once you start comparing results for metagenomes (say you are interested in the phylogenetic reconstruction) different versions of the NR used for the underlying data will lead to incorrect comparison results as older versions of NR will miss certain organisms and or annotations.<br />
<br />
=== How long does it take to analyze my Metagenome? ===<br />
The answer depends on two factors a) the size of your data set and b) the current server load. Under optimal conditions, it takes about 18 hours to run a 100 million basepair 454 metagenome through the pipeline.<br />
<br />
=== What parameters should I use to analyze my data? ===<br />
The answer depends on your sample. In any case we recommend that you modify e-value, minimal alignment length and percent identity requirements for the BLAST results underlying the results. The effects of this are different for each sample. Depending on sample complexity, sample size, number of species an diversity of species present your results will vary dramatically when modifying these parameters. For RNA based phylogenetic reconstruction, we recommend requiring a minimum alignment length of 50bp for exact matches.</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0&diff=1829MG RAST v2.02008-06-20T17:40:51Z<p>FolkerMeyer: /* Frequently asked questions (FAQ)]] */</p>
<hr />
<div>== MG-RAST v2.0 Homepage ==<br />
<br />
=== What is MG-RAST ( Executive Summary) ===<br />
<br />
MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs.<br />
<br />
In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases.<br />
<br />
Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes.<br />
<br />
=== Overview ===<br />
<br />
The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes.<br />
<br />
The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database.<br />
<br />
User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats.<br />
<br />
To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address.<br />
<br />
<br />
=== What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) ===<br />
We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0:<br />
<br />
* Significant improvements of user interface responsiveness and overall performance.<br />
* The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use.<br />
* The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]).<br />
* The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly.<br />
* The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions.<br />
* We have added a recruitment plot feature, plotting fragments against microbial genomes.<br />
* We have added the ability to view all BLAST hits for a fragment and show the individual BLAST alignments.<br />
* The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview).<br />
* We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0<br />
* We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database])<br />
* Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. <br />
* Support for user driven creation and maintenance of groups.<br />
* The ability to support arbitrary sets and versions of databases.<br />
* Many small detailed fixes and improvements.<br />
<br />
<br />
== Databases used ==<br />
* [http://www.theseed.org SEED non redundant protein database]<br />
* [http://greengenes.lbl.gov/ GREENGENES]<br />
* [http://rdp.cme.msu.edu/ RDP-II]<br />
* [http://www.arb-silva.de/ SILVA]<br />
<br />
== Standard Compliance ==<br />
We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO"<br />
<br />
== Navigating MG-RAST v2.0 ==<br />
[this will be a simple graphical overview of the pages and their links]<br />
<br />
== Manual for MG-RAST v2.0 ==<br />
Separate page<br />
== Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) ==<br />
Separate page<br />
<br />
== Availability==<br />
Using MG-RAST is free for all users. We provide privacy for the data submitted and <br />
<br />
MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. <br />
<br />
== Frequently asked questions (FAQ) ==<br />
<br />
We provide a list of frequently asked questions at [[MG_RAST_v2.0_FAQ]].<br />
<br />
== Contact ==<br />
Once logged in to the system, the address of the MG-RAST system will be available to all users.</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0&diff=1828MG RAST v2.02008-06-20T17:40:40Z<p>FolkerMeyer: </p>
<hr />
<div>== MG-RAST v2.0 Homepage ==<br />
<br />
=== What is MG-RAST ( Executive Summary) ===<br />
<br />
MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs.<br />
<br />
In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases.<br />
<br />
Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes.<br />
<br />
=== Overview ===<br />
<br />
The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes.<br />
<br />
The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database.<br />
<br />
User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats.<br />
<br />
To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address.<br />
<br />
<br />
=== What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) ===<br />
We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0:<br />
<br />
* Significant improvements of user interface responsiveness and overall performance.<br />
* The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use.<br />
* The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]).<br />
* The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly.<br />
* The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions.<br />
* We have added a recruitment plot feature, plotting fragments against microbial genomes.<br />
* We have added the ability to view all BLAST hits for a fragment and show the individual BLAST alignments.<br />
* The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview).<br />
* We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0<br />
* We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database])<br />
* Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. <br />
* Support for user driven creation and maintenance of groups.<br />
* The ability to support arbitrary sets and versions of databases.<br />
* Many small detailed fixes and improvements.<br />
<br />
<br />
== Databases used ==<br />
* [http://www.theseed.org SEED non redundant protein database]<br />
* [http://greengenes.lbl.gov/ GREENGENES]<br />
* [http://rdp.cme.msu.edu/ RDP-II]<br />
* [http://www.arb-silva.de/ SILVA]<br />
<br />
== Standard Compliance ==<br />
We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO"<br />
<br />
== Navigating MG-RAST v2.0 ==<br />
[this will be a simple graphical overview of the pages and their links]<br />
<br />
== Manual for MG-RAST v2.0 ==<br />
Separate page<br />
== Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) ==<br />
Separate page<br />
<br />
== Availability==<br />
Using MG-RAST is free for all users. We provide privacy for the data submitted and <br />
<br />
MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. <br />
<br />
== Frequently asked questions (FAQ)]] ==<br />
<br />
We provide a list of frequently asked questions at [[MG_RAST_v2.0_FAQ]].<br />
<br />
== Contact ==<br />
Once logged in to the system, the address of the MG-RAST system will be available to all users.</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0&diff=1827MG RAST v2.02008-06-20T17:40:04Z<p>FolkerMeyer: </p>
<hr />
<div>== MG-RAST v2.0 Homepage ==<br />
<br />
=== What is MG-RAST ( Executive Summary) ===<br />
<br />
MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs.<br />
<br />
In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases.<br />
<br />
Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes.<br />
<br />
=== Overview ===<br />
<br />
The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes.<br />
<br />
The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database.<br />
<br />
User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats.<br />
<br />
To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address.<br />
<br />
<br />
=== What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) ===<br />
We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0:<br />
<br />
* Significant improvements of user interface responsiveness and overall performance.<br />
* The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use.<br />
* The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]).<br />
* The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly.<br />
* The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions.<br />
* We have added a recruitment plot feature, plotting fragments against microbial genomes.<br />
* We have added the ability to view all BLAST hits for a fragment and show the individual BLAST alignments.<br />
* The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview).<br />
* We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0<br />
* We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database])<br />
* Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. <br />
* Support for user driven creation and maintenance of groups.<br />
* The ability to support arbitrary sets and versions of databases.<br />
* Many small detailed fixes and improvements.<br />
<br />
<br />
== Databases used ==<br />
* [http://www.theseed.org SEED non redundant protein database]<br />
* [http://greengenes.lbl.gov/ GREENGENES]<br />
* [http://rdp.cme.msu.edu/ RDP-II]<br />
* [http://www.arb-silva.de/ SILVA]<br />
<br />
== Standard Compliance ==<br />
We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO"<br />
<br />
== Navigating MG-RAST v2.0 ==<br />
[this will be a simple graphical overview of the pages and their links]<br />
<br />
== Manual for MG-RAST v2.0 ==<br />
Separate page<br />
== Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) ==<br />
Separate page<br />
<br />
== Availability==<br />
Using MG-RAST is free for all users. We provide privacy for the data submitted and <br />
<br />
MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. <br />
<br />
== [[MG_RAST_v2.0_FAQ]] ==<br />
<br />
#| Frequently asked questions (FAQ)]] ==<br />
<br />
== Contact ==<br />
Once logged in to the system, the address of the MG-RAST system will be available to all users.</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0&diff=1826MG RAST v2.02008-06-20T17:38:41Z<p>FolkerMeyer: </p>
<hr />
<div>== MG-RAST v2.0 Homepage ==<br />
<br />
=== What is MG-RAST ( Executive Summary) ===<br />
<br />
MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs.<br />
<br />
In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases.<br />
<br />
Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes.<br />
<br />
=== Overview ===<br />
<br />
The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes.<br />
<br />
The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database.<br />
<br />
User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats.<br />
<br />
To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address.<br />
<br />
<br />
=== What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) ===<br />
We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0:<br />
<br />
* Significant improvements of user interface responsiveness and overall performance.<br />
* The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use.<br />
* The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]).<br />
* The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly.<br />
* The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions.<br />
* We have added a recruitment plot feature, plotting fragments against microbial genomes.<br />
* We have added the ability to view all BLAST hits for a fragment and show the individual BLAST alignments.<br />
* The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview).<br />
* We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0<br />
* We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database])<br />
* Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. <br />
* Support for user driven creation and maintenance of groups.<br />
* The ability to support arbitrary sets and versions of databases.<br />
* Many small detailed fixes and improvements.<br />
<br />
<br />
== Databases used ==<br />
* [http://www.theseed.org SEED non redundant protein database]<br />
* [http://greengenes.lbl.gov/ GREENGENES]<br />
* [http://rdp.cme.msu.edu/ RDP-II]<br />
* [http://www.arb-silva.de/ SILVA]<br />
<br />
== Standard Compliance ==<br />
We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO"<br />
<br />
== Navigating MG-RAST v2.0 ==<br />
[this will be a simple graphical overview of the pages and their links]<br />
<br />
== Manual for MG-RAST v2.0 ==<br />
Separate page<br />
== Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) ==<br />
Separate page<br />
<br />
== Availability==<br />
Using MG-RAST is free for all users. We provide privacy for the data submitted and <br />
<br />
MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. <br />
<br />
== [[MG_RAST_v2.0_FAQ| Frequently asked questions (FAQ)]] ==<br />
<br />
== Contact ==<br />
Once logged in to the system, the address of the MG-RAST system will be available to all users.</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0&diff=1825MG RAST v2.02008-06-20T17:37:52Z<p>FolkerMeyer: /* Frequently asked questions (FAQ) */</p>
<hr />
<div>== MG-RAST v2.0 Homepage ==<br />
<br />
=== What is MG-RAST ( Executive Summary) ===<br />
<br />
MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs.<br />
<br />
In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases.<br />
<br />
Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes.<br />
<br />
=== Overview ===<br />
<br />
The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes.<br />
<br />
The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database.<br />
<br />
User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats.<br />
<br />
To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address.<br />
<br />
<br />
=== What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) ===<br />
We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0:<br />
<br />
* Significant improvements of user interface responsiveness and overall performance.<br />
* The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use.<br />
* The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]).<br />
* The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly.<br />
* The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions.<br />
* We have added a recruitment plot feature, plotting fragments against microbial genomes.<br />
* We have added the ability to view all BLAST hits for a fragment and show the individual BLAST alignments.<br />
* The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview).<br />
* We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0<br />
* We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database])<br />
* Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. <br />
* Support for user driven creation and maintenance of groups.<br />
* The ability to support arbitrary sets and versions of databases.<br />
* Many small detailed fixes and improvements.<br />
<br />
<br />
== Databases used ==<br />
* [http://www.theseed.org SEED non redundant protein database]<br />
* [http://greengenes.lbl.gov/ GREENGENES]<br />
* [http://rdp.cme.msu.edu/ RDP-II]<br />
* [http://www.arb-silva.de/ SILVA]<br />
<br />
== Standard Compliance ==<br />
We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO"<br />
<br />
== Navigating MG-RAST v2.0 ==<br />
[this will be a simple graphical overview of the pages and their links]<br />
<br />
== Manual for MG-RAST v2.0 ==<br />
Separate page<br />
== Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) ==<br />
Separate page<br />
<br />
== Availability==<br />
Using MG-RAST is free for all users. We provide privacy for the data submitted and <br />
<br />
MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. <br />
<br />
== [[MG_RAST_v2.0_FAQ Frequently asked questions (FAQ)]] ==<br />
<br />
== Contact ==<br />
Once logged in to the system, the address of the MG-RAST system will be available to all users.</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0_FAQ&diff=1824MG RAST v2.0 FAQ2008-06-20T17:37:28Z<p>FolkerMeyer: </p>
<hr />
<div>=== What are projects? ===<br />
Projects are related sets of metagenomes. If you for example plan on studying a set of samples from a chronoseries, it might me useful to group them into a project.<br />
<br />
=== What level of privacy does MG-RAST v2.0 provide? ===<br />
We provide password control and the ability for the submitting entity to control access on a username/password basis to the submitted data sets.<br />
<br />
=== Do you support BLASTing against my private database XYZ? ===<br />
We currently do not explicitly support this, however the underlying software design end system architecture support this. <br />
<br />
=== How frequently do you update the underlying NR for MG-RAST? ===<br />
With version 2.0 we have added the support for multiple concurrent sets of sequence similarity results to be stored per metagenome. We can add results for newer NRs. However once you start comparing results for metagenomes (say you are interested in the phylogenetic reconstruction) different versions of the NR used for the underlying data will lead to incorrect comparison results as older versions of NR will miss certain organisms and or annotations.</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0&diff=1823MG RAST v2.02008-06-20T17:20:53Z<p>FolkerMeyer: </p>
<hr />
<div>== MG-RAST v2.0 Homepage ==<br />
<br />
=== What is MG-RAST ( Executive Summary) ===<br />
<br />
MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs.<br />
<br />
In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases.<br />
<br />
Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes.<br />
<br />
=== Overview ===<br />
<br />
The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes.<br />
<br />
The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database.<br />
<br />
User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats.<br />
<br />
To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address.<br />
<br />
<br />
=== What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) ===<br />
We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0:<br />
<br />
* Significant improvements of user interface responsiveness and overall performance.<br />
* The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use.<br />
* The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]).<br />
* The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly.<br />
* The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions.<br />
* We have added a recruitment plot feature, plotting fragments against microbial genomes.<br />
* We have added the ability to view all BLAST hits for a fragment and show the individual BLAST alignments.<br />
* The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview).<br />
* We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0<br />
* We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database])<br />
* Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. <br />
* Support for user driven creation and maintenance of groups.<br />
* The ability to support arbitrary sets and versions of databases.<br />
* Many small detailed fixes and improvements.<br />
<br />
<br />
== Databases used ==<br />
* [http://www.theseed.org SEED non redundant protein database]<br />
* [http://greengenes.lbl.gov/ GREENGENES]<br />
* [http://rdp.cme.msu.edu/ RDP-II]<br />
* [http://www.arb-silva.de/ SILVA]<br />
<br />
== Standard Compliance ==<br />
We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO"<br />
<br />
== Navigating MG-RAST v2.0 ==<br />
[this will be a simple graphical overview of the pages and their links]<br />
<br />
== Manual for MG-RAST v2.0 ==<br />
Separate page<br />
== Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) ==<br />
Separate page<br />
<br />
== Availability==<br />
Using MG-RAST is free for all users. We provide privacy for the data submitted and <br />
<br />
MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. <br />
<br />
== Frequently asked questions (FAQ) ==<br />
Separate Page<br />
<br />
== Contact ==<br />
Once logged in to the system, the address of the MG-RAST system will be available to all users.</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0&diff=1822MG RAST v2.02008-06-20T17:20:16Z<p>FolkerMeyer: </p>
<hr />
<div>== MG-RAST v2.0 Homepage ==<br />
<br />
=== What is MG-RAST ( Executive Summary) ===<br />
<br />
MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs.<br />
<br />
In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases.<br />
<br />
Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes.<br />
<br />
=== Overview ===<br />
<br />
The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes.<br />
<br />
The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database.<br />
<br />
User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats.<br />
<br />
To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address.<br />
<br />
<br />
=== What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) ===<br />
We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0:<br />
<br />
* Significant improvements of user interface responsiveness and overall performance.<br />
* The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use.<br />
* The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]).<br />
* The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly.<br />
* The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions.<br />
* We have added a recruitment plot feature, plotting fragments against microbial genomes.<br />
* We have added the ability to view all BLAST hits for a fragment and show the individual BLAST alignments.<br />
* The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview).<br />
* We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0<br />
* We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database])<br />
* Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. <br />
* Support for user driven creation and maintenance of groups.<br />
* The ability to support arbitrary sets and versions of databases.<br />
* Many small detailed fixes and improvements.<br />
<br />
<br />
== Databases used ==<br />
* [http://www.theseed.org SEED non redundant protein database]<br />
* [http://greengenes.lbl.gov/ GREENGENES]<br />
* [http://rdp.cme.msu.edu/ RDP-II]<br />
* [http://www.arb-silva.de/ SILVA]<br />
<br />
== Standard Compliance ==<br />
We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO"<br />
<br />
== Page Overview ==<br />
[this will be a simple graphical overview of the pages and their links]<br />
<br />
== Manual for MG-RAST v2.0 ==<br />
Separate page<br />
== Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) ==<br />
Separate page<br />
<br />
== Availability==<br />
Using MG-RAST is free for all users. We provide privacy for the data submitted and <br />
<br />
MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. <br />
<br />
== Frequently asked questions (FAQ) ==<br />
Separate Page<br />
<br />
== Contact ==<br />
Once logged in to the system, the address of the MG-RAST system will be available to all users.</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0&diff=1821MG RAST v2.02008-06-20T17:19:43Z<p>FolkerMeyer: </p>
<hr />
<div>== MG-RAST v2.0 Homepage ==<br />
<br />
=== What is MG-RAST ( Executive Summary) ===<br />
<br />
MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs.<br />
<br />
In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases.<br />
<br />
Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes.<br />
<br />
=== Overview ===<br />
<br />
The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes.<br />
<br />
The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database.<br />
<br />
User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats.<br />
<br />
To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address.<br />
<br />
<br />
=== What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) ===<br />
We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0:<br />
<br />
* Significant improvements of user interface responsiveness and overall performance.<br />
* The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use.<br />
* The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]).<br />
* The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly.<br />
* The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions.<br />
* We have added a recruitment plot feature, plotting fragments against microbial genomes.<br />
* We have added the ability to view all BLAST hits for a fragment and show the individual BLAST alignments.<br />
* The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview).<br />
* We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0<br />
* We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database])<br />
* Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. <br />
* Support for user driven creation and maintenance of groups.<br />
* The ability to support arbitrary sets and versions of databases.<br />
* Many small detailed fixes and improvements.<br />
<br />
<br />
== Databases used ==<br />
* [http://www.theseed.org SEED non redundant protein database]<br />
* [http://greengenes.lbl.gov/ GREENGENES]<br />
* [http://rdp.cme.msu.edu/ RDP-II]<br />
* [http://www.arb-silva.de/ SILVA]<br />
<br />
== Standard Compliance ==<br />
We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO"<br />
<br />
== - Page Overview ==<br />
[this will be a simple graphical overview of the pages and their links]<br />
<br />
== Manual for MG-RAST v2.0 ==<br />
Separate page<br />
== Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) ==<br />
Separate page<br />
<br />
== Availability==<br />
Using MG-RAST is free for all users. We provide privacy for the data submitted and <br />
<br />
MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. <br />
<br />
=== Frequently asked questions (FAQ) ===<br />
Separate Page<br />
<br />
=== Contact ===<br />
Once logged in to the system, the address of the MG-RAST system will be available to all users.</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0&diff=1820MG RAST v2.02008-06-20T17:18:02Z<p>FolkerMeyer: </p>
<hr />
<div>== MG-RAST v2.0 Homepage ==<br />
<br />
=== What is MG-RAST ( Executive Summary) ===<br />
<br />
MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs.<br />
<br />
In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases.<br />
<br />
Both the submitted data and the MG-RAST analysis can be shared with other users or "published" to the public on the server, we provide stable unique identifiers for public metagenomes.<br />
<br />
=== Overview ===<br />
<br />
The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes.<br />
<br />
The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database.<br />
<br />
User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats.<br />
<br />
To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address.<br />
<br />
<br />
=== What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) ===<br />
We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0:<br />
<br />
* Significant improvements of user interface responsiveness and overall performance.<br />
* The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use.<br />
* The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]).<br />
* The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly.<br />
* The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions.<br />
* We have added a recruitment plot feature, plotting fragments against microbial genomes.<br />
* We have added the ability to view all BLAST hits for a fragment and show the individual BLAST alignments.<br />
* The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview).<br />
* We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0<br />
* We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database])<br />
* Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. <br />
* Support for user driven creation and maintenance of groups.<br />
* The ability to support arbitrary sets and versions of databases.<br />
* Many small detailed fixes and improvements.<br />
<br />
<br />
== Databases used ==<br />
* [http://www.theseed.org SEED non redundant protein database]<br />
* [http://greengenes.lbl.gov/ GREENGENES]<br />
* [http://rdp.cme.msu.edu/ RDP-II]<br />
* [http://www.arb-silva.de/ SILVA]<br />
<br />
== Standard Compliance ==<br />
We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO"<br />
<br />
== - Page Overview ==<br />
[this will be a simple graphical overview of the pages and their links]<br />
<br />
== Manual for MG-RAST v2.0 ==<br />
Separate page<br />
== Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) ==<br />
Separate page<br />
<br />
== Availability==<br />
Using MG-RAST is free for all users. We provide privacy for the data submitted and <br />
<br />
MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. <br />
<br />
=== FAQ<br />
- Contact</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0&diff=1819MG RAST v2.02008-06-20T17:14:50Z<p>FolkerMeyer: </p>
<hr />
<div>== MG-RAST v2.0 Homepage ==<br />
<br />
=== What is MG-RAST ===<br />
<br />
MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs.<br />
<br />
In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases.<br />
<br />
<br />
=== Overview ===<br />
<br />
The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes.<br />
<br />
The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database.<br />
<br />
User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats.<br />
<br />
To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address.<br />
<br />
<br />
=== What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) ===<br />
We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0:<br />
<br />
* Significant improvements of user interface responsiveness and overall performance.<br />
* The ability to <strong>"publish" metagenomes on the MG-RAST server</strong> for public use.<br />
* The ability to <strong>download subsets</strong> of fragments as fasta (eg. all fragments matching a given eg. a [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or a [http://www.theseed.org/wiki/Glossary#Functional_role functional role]).<br />
* The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly.<br />
* The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions.<br />
* We have added a recruitment plot feature, plotting fragments against microbial genomes.<br />
* We have added the ability to view all BLAST hits for a fragment and show the individual BLAST alignments.<br />
* The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview).<br />
* We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0<br />
* We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database])<br />
* Added the <strong>Invite a friend feature</strong> to share data that you submitted with other users by just entering their email addresses. <br />
* Support for user driven creation and maintenance of groups.<br />
* Many small detailed fixes and improvements.<br />
<br />
== Databases used ==<br />
* [http://www.theseed.org SEED non redundant protein database]<br />
* [http://greengenes.lbl.gov/ GREENGENES]<br />
* [http://rdp.cme.msu.edu/ RDP-II]<br />
* [http://www.arb-silva.de/ SILVA]<br />
<br />
== Standard Compliance ==<br />
We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO"<br />
<br />
== - Page Overview ==<br />
[this will be a simple graphical overview of the pages and their links]<br />
== Manual for MG-RAST v2.0 ==<br />
Separate page<br />
== Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) ==<br />
Separate page<br />
<br />
== Availability==<br />
Using MG-RAST is free for all users. We provide privacy for the data submitted and <br />
<br />
MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. <br />
<br />
=== FAQ<br />
- Contact</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0&diff=1818MG RAST v2.02008-06-20T17:06:55Z<p>FolkerMeyer: </p>
<hr />
<div>== MG-RAST v2.0 Homepage ==<br />
<br />
=== What is MG-RAST ===<br />
<br />
MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs.<br />
<br />
In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases.<br />
<br />
<br />
=== Overview ===<br />
<br />
The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes.<br />
<br />
The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database.<br />
<br />
User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats.<br />
<br />
To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address.<br />
<br />
<br />
=== What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) ===<br />
We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0:<br />
<br />
* Significant improvements of user interface responsiveness and overall performance.<br />
* ability to see/download fragments and see blast alignments<br />
* The ability to download subsets of fragments as fasta (eg. all fragments matching a given [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or [http://www.theseed.org/wiki/Glossary#Functional_role functional role]).<br />
* The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly.<br />
* The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions.<br />
* We have added a recruitment plot feature, plotting fragments against microbial genomes.<br />
* The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview).<br />
* We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0<br />
* We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database])<br />
* Invite a friend feature to share data that you submitted with other users by just entering their email addresses. <br />
* Support for user driven creation and maintenance of groups.<br />
* many small detailed fixes<br />
<br />
=== Databases used ===<br />
* [http://www.theseed.org SEED non redundant protein database]<br />
* [http://greengenes.lbl.gov/ GREENGENES]<br />
* [http://rdp.cme.msu.edu/ RDP-II]<br />
* [http://www.arb-silva.de/ SILVA]<br />
<br />
=== Standard Compliance ===<br />
We are currently working with Dawn Fields and Renzo Kottmann from the GSC to support a version of "ANDREAS PLEASE SUPPLY THIS INFO"<br />
<br />
=== - Page Overview ===<br />
[this will be a simple graphical overview of the pages and their links]<br />
=== Manual for MG-RAST v2.0 ===<br />
=== Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) ===<br />
=== Availability===<br />
MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. <br />
<br />
=== FAQ<br />
- Contact</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0&diff=1817MG RAST v2.02008-06-20T17:00:48Z<p>FolkerMeyer: </p>
<hr />
<div>== MG-RAST v2.0 Homepage ==<br />
<br />
=== What is MG-RAST ===<br />
<br />
MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs.<br />
<br />
In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases.<br />
<br />
<br />
=== Overview ===<br />
<br />
The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes.<br />
<br />
The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database.<br />
<br />
User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats.<br />
<br />
To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address.<br />
<br />
<br />
=== What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) ===<br />
We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0:<br />
<br />
* Significant improvements of user interface responsiveness and overall performance.<br />
* ability to see/download fragments and see blast alignments<br />
* The ability to download subsets of fragments as fasta (eg. all fragments matching a given [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or [http://www.theseed.org/wiki/Glossary#Functional_role functional role]).<br />
* The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly.<br />
* The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions.<br />
* We have added a recruitment plot feature, plotting fragments against microbial genomes.<br />
* The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview).<br />
* We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0<br />
* We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database])<br />
* Invite a friend feature to share data that you submitted with other users by just entering their email addresses. <br />
* Support for user driven creation and maintenance of groups.<br />
* many small detailed fixes<br />
<br />
=== Databases used ===<br />
* [http://www.theseed.org SEED non redundant protein database]<br />
* [http://greengenes.lbl.gov/ GREENGENES]<br />
* [3 RDP-II]<br />
* [http://www.arb-silva.de/ SILVA]<br />
<br />
=== Standard Compliance ===<br />
=== - Page Overview ===<br />
[this will be a simple graphical overview of the pages and their links]<br />
=== Manual for MG-RAST v2.0 ===<br />
=== Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) ===<br />
=== Availability===<br />
MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. <br />
<br />
=== FAQ<br />
- Contact</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0&diff=1816MG RAST v2.02008-06-20T16:18:15Z<p>FolkerMeyer: </p>
<hr />
<div>== MG-RAST v2.0 Homepage ==<br />
<br />
=== What is MG-RAST ===<br />
<br />
MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs.<br />
<br />
In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases.<br />
<br />
<br />
=== Overview ===<br />
<br />
The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes.<br />
<br />
The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database.<br />
<br />
User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats.<br />
<br />
To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address.<br />
<br />
<br />
=== What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) ===<br />
We have gone through several rounds of feedback with users of version 1.2 (Many thanks to all who send suggestions!) and have included the following new capabilities in version 2.0:<br />
<br />
* The ability to download subsets of fragments as fasta (eg. all fragments matching a given [http://www.theseed.org/wiki/Glossary#Subsystem subsystem] or [http://www.theseed.org/wiki/Glossary#Functional_role functional role]<br />
* The ability to modify parameters for sequence comparison underlying both metabolic reconstruction and phylogenetic reconstruction on the fly.<br />
* The same capability for the heatmap style comparisons of both metabolisms and phylogenetic reconstructions.<br />
* We have added a recruitment plot feature, plotting fragments against microbial genomes.<br />
* The ability to use [http://www.genome.ad.jp/kegg/kegg2.html KEGG] maps map explore and compare metabolic reconstructions on several hierarchy levels (e.g. the high level metabolism overview).<br />
* We have changed the pipeline that computes the underlying data so all numbers/percentages/comparisons/etc. will have changed if you look at your data in v2.0<br />
* We have also updated the underlying databases. Most notably the [http://www.theseed.org SEED] NR no longer from represents the status from 2006, we have added the [http://www.arb-silva.de/ Silva RNA database])<br />
* support for groups and inviting friends to look at data<br />
* much faster user interface <br />
* ability to see/download fragments and see blast alignments<br />
* many small detailed fixes<br />
<br />
=== Databases used ===<br />
<br />
=== Standard Compliance ===<br />
=== - Page Overview ===<br />
[this will be a simple graphical overview of the pages and their links]<br />
=== Manual for MG-RAST v2.0 ===<br />
=== Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) ===<br />
=== Availability===<br />
MG-RAST is open source. While we currently do not provide a defined release, current snapshots of the system are available via CVS. <br />
<br />
=== FAQ<br />
- Contact</div>FolkerMeyer /w/index.php?title=MG_RAST_v2.0&diff=1815MG RAST v2.02008-06-20T15:53:30Z<p>FolkerMeyer: </p>
<hr />
<div>== MG-RAST v2.0 Homepage ==<br />
<br />
=== What is MG-RAST ===<br />
<br />
MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating metagenome samples. It is the only service that we are aware of that will handle both short reads (notably reads of 109 or 230 basepairs from a [http://en.wikipedia.org/wiki/454_life_sciences#Technology 454] instrument) and longer [http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods Sanger] reads or even assembled short contigs.<br />
<br />
In the MG-RAST analysis the fragments in a given sample will be compared to protein, RNA and subsystem databases.<br />
<br />
<br />
=== Overview ===<br />
<br />
The MG-RAST system will utilize data structures and software generated in the context of [http://www.theseed.org The SEED] and [http://www.nmpdr.org NMPDR] to provide annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes.<br />
<br />
The service is built as a modified version of the [http://rast.nmpdr.org RAST] server, which was originally designed to support high-quality annotation of complete or draft microbial genomes. We have adapted this technology for the analysis of metagenomes. In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II, SILVA, and European ribosomal RNA database.<br />
<br />
User submission and analysis are confidential, although each user may optionally allow a collaborative environment that enables multiple users to share datasets. In addition, users can also allow public access and request long-term storage of their metagenomic samples on the server. The server provides unique IDs for metagenomes and the sequences they contain and provides a stable mechanism for linking to. All data and analysis are available for download in a variety of different formats.<br />
<br />
To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address.<br />
<br />
<br />
=== What's new? (Changes from MG-RAST v1.2 to MG-RAST v2.0) ===<br />
<br />
=== Standard Compliance ===<br />
=== - Page Overview ===<br />
[this will be a simple graphical overview of the pages and their links]<br />
=== Manual for MG-RAST v2.0 ===<br />
=== Tutorial (Using MG-RAST-v2.0 to analyze my metagenome sample) ===<br />
=== FAQ<br />
- Contact</div>FolkerMeyer /w/index.php?title=Papers_that_use_the_SEED&diff=1804Papers that use the SEED2008-04-16T13:22:56Z<p>FolkerMeyer: </p>
<hr />
<div>=2005=<br />
# Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) Oct 7;33(17):5691-702. [http://www.ncbi.nlm.nih.gov/pubmed/16214803 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/33/17/5691 NAR] [http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplemental Online Material] <br />
=2006=<br />
# Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., Chan, A.M., Haynes, M., Kelley, S., Liu, H. et al. (2006) The marine viromes of four oceanic regions. PLoS Biol, 4. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=The%20marine%20viromes%20of%20four%20oceanic%20regions&cmd_current= PubMed] [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040368&ct=1 PLoS Biology]<br />
# DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., Martinez, A., Sullivan, M.B., Edwards, R., Brito, B.R. et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science, 311, 496-503. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=Community%20genomics%20among%20stratified%20microbial%20assemblages%20in%20the%20ocean%27s%20interior&cmd_current= PubMed]<br />
# Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander, E.C., Jr. and Rohwer, F. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 7, 57. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16549033&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/7/57 BioMed Central]<br />
# Gerdes, S., R. Edwards, M. Kubal, M. Fonstein, R. Stevens, and A. Osterman. (2006). Essential genes on metabolic maps. Curr Opin Biotechnol 17:448-56. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16978855 PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KWTFBB-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3067cb821f4b494047d5270860f5557c Science Direct]<br />
# Gerdes, S., Kurnasov, O., Shatalin, K., Polanuyer, B., Sloutsky, R., Vonstein, V., Overbeek, R., and A.L. Osterman (2006). Comparative Genomics of NAD Biosynthesis in Cyanobacteria. J. Bacteriol. 188: 3012-3023. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16585762&cmd_current= PubMed] [http://jb.asm.org/cgi/content/abstract/188/8/3012 J. Bact]<br />
# Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S., (2006). Experimental and computational assessment of conditionally essential genes in E. coli. J Bacteriol. 188(23):8259-71. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17012394 PubMed] [http://jb.asm.org/cgi/content/full/188/23/8259?view=long&pmid=17012394 JBact]<br />
# Krause, L., Diaz, N.N., Bartels, D., Edwards, R.A., Puhler, A., Rohwer, F., Meyer, F. and Stoye, J. (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22, e281. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16873483&cmd_current= PubMed] [http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e281 NAR]<br />
# Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162.<br />
# El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V. (2006) Discovery of a new prokaryotic type I GTP cyclohydrolase family. J Biol Chem. Dec 8;281(49):37586-93. Epub 2006 Oct 10. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17032654&cmd_current= PubMed] [http://www.jbc.org/cgi/content/full/281/49/37586 JBC]# Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, P., Jones, R., Robeson, M., Edwards, R., Felts, B., Rayhawk, S. et al. (2007) Metagenomic and small-subunit RNA surveys reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol, 73, 7059-7066. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17827313&cmd_current= PubMed] [http://aem.asm.org/cgi/content/full/73/21/7059?view=long&pmid=17827313 AEM]<br />
# Yang, C., D. A. Rodionov, X. Li, O. N. Laikova, M. S. Gelfand, O. P. Zagnitko, M. F. Romine, A. Y. Obraztsova, K. H. Nealson, and A. L. Osterman. (2006). Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem 281:29872-85. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16857666 PubMed] [http://www.jbc.org/cgi/content/full/281/40/29872 JBC]<br />
<br />
=2007=<br />
# de Crecy-Lagard V, Hanson AD. (2007) Finding novel metabolic genes through plant-prokaryote phylogenomics. Trends Microbiol. Dec;15(12):563-70. Epub 2007 Nov 9. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17997099&cmd_current= PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-4R3BW70-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=45c7be528111535816858125516a93ad Trends]<br />
# de Crecy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD. (2007) Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics. Jul 23;8:245.[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17645794&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/8/245 Biomed Central]<br />
# Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. (2007) Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation.Genome Res. Sep;17(9):1362-77. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17690205 PubMed] [http://www.genome.org/cgi/content/full/17/9/1362 Genome Research]<br />
# McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes SY, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman AL, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko OP, Xia F, Zinner J, Overbeek R, Stevens R.(2007) The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53 [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17145713 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D347 NAR]<br />
# Osterman, A., and T. Begley. (2007). A Subsystems-based approach to the identification of drug targets in bacterial pathogens, p. 132-170. In H.Boshoff and C.Barry (ed.), Progress in Drug Research, vol. 64. Birkhauser Verlag, Basel. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17195474 PubMed]<br />
# Dmitry A. Rodionov, Oleg V. Kurnasov, Boguslaw Stec, Yan Wang, Mary F. Roberts, and Andrei L. Osterman (2007) Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. . Proc Natl Acad Sci U S A. Mar 13;104(11):4279-84. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17360515 PubMed] [http://www.pnas.org/cgi/content/full/104/11/4279 PNAS]<br />
# Wegley, L., Breitbart, M., Edwards, R. and Rohwer, F. (2007) Functional and taxonimic analysis of coral-associated microbes using metagenomic analysis. Environ Microbiol, 9, 2707-2719. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17922755&cmd_current= PubMed] [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1462-2920.2007.01383.x Environ Microbiol]<br />
# Yang C, Rodionov DA, Rodionova IA, Li X, Osterman AL. (2007) Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways., J Bacteriol. 2007 Dec 21; [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=18156253&cmd_current= PubMed] [http://jb.asm.org/cgi/reprint/JB.01469-07v1?view=long&pmid=18156253 JBact]<br />
# JR. Yates III and AL. Osterman (2007) Introduction: advances in genomics and proteomics. Chem Rev. Aug;107(8):3363-6. Epub 2007 Jul 21. [http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/cr068201u ACS]<br />
# DeJongh, M., Formsma, K., Boillot, P., Gould, J., Rycenga M., and Best, A. (2007) Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics 2007 [http://www.ncbi.nlm.nih.gov/pubmed/17462086 Pubmed] [http://www.biomedcentral.com/1471-2105/8/139 BMC Bioinformatics]<br />
<br />
=2008=<br />
# Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. (2008) , The RAST Server: rapid annotations using subsystems technology. BMC Genomics [http://www.ncbi.nlm.nih.gov/pubmed/18261238 Pubmed] [http://www.biomedcentral.com/1471-2164/9/75 BMC Genomics]<br />
# Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM, Furlan M, Desnues C, Haynes M, Li L, McDaniel L, Moran MA, Nelson KE, Nilsson C, Olson R, Paul J, Brito BR, Ruan Y, Swan BK, Stevens R, Valentine DL, Thurber RV, Wegley L, White BA, Rohwer F., (2008) Functional metagenomic profiling of nine biomes., Nature 2008 Apr 3;452(7187):629-32, [http://www.ncbi.nlm.nih.gov/pubmed/18337718 Pubmed] [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature06810.html Nature]<br />
<br />
<br />
=In press=<br />
# Desnues CG, B Rodriguez-Brito, S Rayhawk, S Kelley, T Tran, M Haynes, H Liu, D Hall, FE Angly, RA Edwards, RB Thurber, P Reid, J Siefert, V Souza, DL Valentine, BK Swan, M Breitbart, F Rohwer (2008; accepted) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature In press.<br />
# Mou, X.S., S., Edwards, R.A., Hodson, R.E. and Moran, M.A. (2007) Generalist Species Dominate Bacterial Carbon Processing in the Coastal Ocean. Nature, In Press.<br />
# Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut.</div>FolkerMeyer /w/index.php?title=Papers_that_use_the_SEED&diff=1803Papers that use the SEED2008-04-16T13:18:44Z<p>FolkerMeyer: /* 2008 */</p>
<hr />
<div>=2005=<br />
# Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) Oct 7;33(17):5691-702. [http://www.ncbi.nlm.nih.gov/pubmed/16214803 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/33/17/5691 NAR] [http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplemental Online Material] <br />
=2006=<br />
# Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., Chan, A.M., Haynes, M., Kelley, S., Liu, H. et al. (2006) The marine viromes of four oceanic regions. PLoS Biol, 4. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=The%20marine%20viromes%20of%20four%20oceanic%20regions&cmd_current= PubMed] [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040368&ct=1 PLoS Biology]<br />
# DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., Martinez, A., Sullivan, M.B., Edwards, R., Brito, B.R. et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science, 311, 496-503. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=Community%20genomics%20among%20stratified%20microbial%20assemblages%20in%20the%20ocean%27s%20interior&cmd_current= PubMed]<br />
# Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander, E.C., Jr. and Rohwer, F. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 7, 57. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16549033&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/7/57 BioMed Central]<br />
# Gerdes, S., R. Edwards, M. Kubal, M. Fonstein, R. Stevens, and A. Osterman. (2006). Essential genes on metabolic maps. Curr Opin Biotechnol 17:448-56. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16978855 PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KWTFBB-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3067cb821f4b494047d5270860f5557c Science Direct]<br />
# Gerdes, S., Kurnasov, O., Shatalin, K., Polanuyer, B., Sloutsky, R., Vonstein, V., Overbeek, R., and A.L. Osterman (2006). Comparative Genomics of NAD Biosynthesis in Cyanobacteria. J. Bacteriol. 188: 3012-3023. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16585762&cmd_current= PubMed] [http://jb.asm.org/cgi/content/abstract/188/8/3012 J. Bact]<br />
# Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S., (2006). Experimental and computational assessment of conditionally essential genes in E. coli. J Bacteriol. 188(23):8259-71. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17012394 PubMed] [http://jb.asm.org/cgi/content/full/188/23/8259?view=long&pmid=17012394 JBact]<br />
# Krause, L., Diaz, N.N., Bartels, D., Edwards, R.A., Puhler, A., Rohwer, F., Meyer, F. and Stoye, J. (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22, e281. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16873483&cmd_current= PubMed] [http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e281 NAR]<br />
# Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162.<br />
# El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V. (2006) Discovery of a new prokaryotic type I GTP cyclohydrolase family. J Biol Chem. Dec 8;281(49):37586-93. Epub 2006 Oct 10. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17032654&cmd_current= PubMed] [http://www.jbc.org/cgi/content/full/281/49/37586 JBC]# Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, P., Jones, R., Robeson, M., Edwards, R., Felts, B., Rayhawk, S. et al. (2007) Metagenomic and small-subunit RNA surveys reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol, 73, 7059-7066. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17827313&cmd_current= PubMed] [http://aem.asm.org/cgi/content/full/73/21/7059?view=long&pmid=17827313 AEM]<br />
# Yang, C., D. A. Rodionov, X. Li, O. N. Laikova, M. S. Gelfand, O. P. Zagnitko, M. F. Romine, A. Y. Obraztsova, K. H. Nealson, and A. L. Osterman. (2006). Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem 281:29872-85. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16857666 PubMed] [http://www.jbc.org/cgi/content/full/281/40/29872 JBC]<br />
<br />
=2007=<br />
# de Crecy-Lagard V, Hanson AD. (2007) Finding novel metabolic genes through plant-prokaryote phylogenomics. Trends Microbiol. Dec;15(12):563-70. Epub 2007 Nov 9. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17997099&cmd_current= PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-4R3BW70-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=45c7be528111535816858125516a93ad Trends]<br />
# de Crecy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD. (2007) Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics. Jul 23;8:245.[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17645794&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/8/245 Biomed Central]<br />
# Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. (2007) Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation.Genome Res. Sep;17(9):1362-77. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17690205 PubMed] [http://www.genome.org/cgi/content/full/17/9/1362 Genome Research]<br />
# McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes SY, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman AL, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko OP, Xia F, Zinner J, Overbeek R, Stevens R.(2007) The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53 [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17145713 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D347 NAR]<br />
# Osterman, A., and T. Begley. (2007). A Subsystems-based approach to the identification of drug targets in bacterial pathogens, p. 132-170. In H.Boshoff and C.Barry (ed.), Progress in Drug Research, vol. 64. Birkhauser Verlag, Basel. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17195474 PubMed]<br />
# Dmitry A. Rodionov, Oleg V. Kurnasov, Boguslaw Stec, Yan Wang, Mary F. Roberts, and Andrei L. Osterman (2007) Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. . Proc Natl Acad Sci U S A. Mar 13;104(11):4279-84. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17360515 PubMed] [http://www.pnas.org/cgi/content/full/104/11/4279 PNAS]<br />
# Wegley, L., Breitbart, M., Edwards, R. and Rohwer, F. (2007) Functional and taxonimic analysis of coral-associated microbes using metagenomic analysis. Environ Microbiol, 9, 2707-2719. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17922755&cmd_current= PubMed] [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1462-2920.2007.01383.x Environ Microbiol]<br />
# Yang C, Rodionov DA, Rodionova IA, Li X, Osterman AL. (2007) Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways., J Bacteriol. 2007 Dec 21; [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=18156253&cmd_current= PubMed] [http://jb.asm.org/cgi/reprint/JB.01469-07v1?view=long&pmid=18156253 JBact]<br />
# JR. Yates III and AL. Osterman (2007) Introduction: advances in genomics and proteomics. Chem Rev. Aug;107(8):3363-6. Epub 2007 Jul 21. [http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/cr068201u ACS]<br />
# DeJongh, M., Formsma, K., Boillot, P., Gould, J., Rycenga M., and Best, A. (2007) Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics 2007 [http://www.ncbi.nlm.nih.gov/pubmed/17462086 Pubmed] [http://www.biomedcentral.com/1471-2105/8/139 BMC Bioinformatics]<br />
<br />
=2008=<br />
# Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. (2008) , The RAST Server: rapid annotations using subsystems technology. BMC Genomics [http://www.ncbi.nlm.nih.gov/pubmed/18261238 Pubmed] [http://www.biomedcentral.com/1471-2164/9/75 BMC Genomics]<br />
<br />
=In press=<br />
# Desnues CG, B Rodriguez-Brito, S Rayhawk, S Kelley, T Tran, M Haynes, H Liu, D Hall, FE Angly, RA Edwards, RB Thurber, P Reid, J Siefert, V Souza, DL Valentine, BK Swan, M Breitbart, F Rohwer (2008; accepted) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature In press.<br />
# Mou, X.S., S., Edwards, R.A., Hodson, R.E. and Moran, M.A. (2007) Generalist Species Dominate Bacterial Carbon Processing in the Coastal Ocean. Nature, In Press.<br />
# Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut.</div>FolkerMeyer /w/index.php?title=Papers_that_use_the_SEED&diff=1802Papers that use the SEED2008-04-16T13:18:12Z<p>FolkerMeyer: /* 2008 */</p>
<hr />
<div>=2005=<br />
# Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) Oct 7;33(17):5691-702. [http://www.ncbi.nlm.nih.gov/pubmed/16214803 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/33/17/5691 NAR] [http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplemental Online Material] <br />
=2006=<br />
# Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., Chan, A.M., Haynes, M., Kelley, S., Liu, H. et al. (2006) The marine viromes of four oceanic regions. PLoS Biol, 4. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=The%20marine%20viromes%20of%20four%20oceanic%20regions&cmd_current= PubMed] [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040368&ct=1 PLoS Biology]<br />
# DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., Martinez, A., Sullivan, M.B., Edwards, R., Brito, B.R. et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science, 311, 496-503. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=Community%20genomics%20among%20stratified%20microbial%20assemblages%20in%20the%20ocean%27s%20interior&cmd_current= PubMed]<br />
# Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander, E.C., Jr. and Rohwer, F. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 7, 57. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16549033&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/7/57 BioMed Central]<br />
# Gerdes, S., R. Edwards, M. Kubal, M. Fonstein, R. Stevens, and A. Osterman. (2006). Essential genes on metabolic maps. Curr Opin Biotechnol 17:448-56. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16978855 PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KWTFBB-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3067cb821f4b494047d5270860f5557c Science Direct]<br />
# Gerdes, S., Kurnasov, O., Shatalin, K., Polanuyer, B., Sloutsky, R., Vonstein, V., Overbeek, R., and A.L. Osterman (2006). Comparative Genomics of NAD Biosynthesis in Cyanobacteria. J. Bacteriol. 188: 3012-3023. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16585762&cmd_current= PubMed] [http://jb.asm.org/cgi/content/abstract/188/8/3012 J. Bact]<br />
# Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S., (2006). Experimental and computational assessment of conditionally essential genes in E. coli. J Bacteriol. 188(23):8259-71. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17012394 PubMed] [http://jb.asm.org/cgi/content/full/188/23/8259?view=long&pmid=17012394 JBact]<br />
# Krause, L., Diaz, N.N., Bartels, D., Edwards, R.A., Puhler, A., Rohwer, F., Meyer, F. and Stoye, J. (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22, e281. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16873483&cmd_current= PubMed] [http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e281 NAR]<br />
# Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162.<br />
# El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V. (2006) Discovery of a new prokaryotic type I GTP cyclohydrolase family. J Biol Chem. Dec 8;281(49):37586-93. Epub 2006 Oct 10. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17032654&cmd_current= PubMed] [http://www.jbc.org/cgi/content/full/281/49/37586 JBC]# Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, P., Jones, R., Robeson, M., Edwards, R., Felts, B., Rayhawk, S. et al. (2007) Metagenomic and small-subunit RNA surveys reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol, 73, 7059-7066. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17827313&cmd_current= PubMed] [http://aem.asm.org/cgi/content/full/73/21/7059?view=long&pmid=17827313 AEM]<br />
# Yang, C., D. A. Rodionov, X. Li, O. N. Laikova, M. S. Gelfand, O. P. Zagnitko, M. F. Romine, A. Y. Obraztsova, K. H. Nealson, and A. L. Osterman. (2006). Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem 281:29872-85. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16857666 PubMed] [http://www.jbc.org/cgi/content/full/281/40/29872 JBC]<br />
<br />
=2007=<br />
# de Crecy-Lagard V, Hanson AD. (2007) Finding novel metabolic genes through plant-prokaryote phylogenomics. Trends Microbiol. Dec;15(12):563-70. Epub 2007 Nov 9. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17997099&cmd_current= PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-4R3BW70-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=45c7be528111535816858125516a93ad Trends]<br />
# de Crecy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD. (2007) Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics. Jul 23;8:245.[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17645794&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/8/245 Biomed Central]<br />
# Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. (2007) Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation.Genome Res. Sep;17(9):1362-77. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17690205 PubMed] [http://www.genome.org/cgi/content/full/17/9/1362 Genome Research]<br />
# McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes SY, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman AL, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko OP, Xia F, Zinner J, Overbeek R, Stevens R.(2007) The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53 [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17145713 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D347 NAR]<br />
# Osterman, A., and T. Begley. (2007). A Subsystems-based approach to the identification of drug targets in bacterial pathogens, p. 132-170. In H.Boshoff and C.Barry (ed.), Progress in Drug Research, vol. 64. Birkhauser Verlag, Basel. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17195474 PubMed]<br />
# Dmitry A. Rodionov, Oleg V. Kurnasov, Boguslaw Stec, Yan Wang, Mary F. Roberts, and Andrei L. Osterman (2007) Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. . Proc Natl Acad Sci U S A. Mar 13;104(11):4279-84. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17360515 PubMed] [http://www.pnas.org/cgi/content/full/104/11/4279 PNAS]<br />
# Wegley, L., Breitbart, M., Edwards, R. and Rohwer, F. (2007) Functional and taxonimic analysis of coral-associated microbes using metagenomic analysis. Environ Microbiol, 9, 2707-2719. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17922755&cmd_current= PubMed] [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1462-2920.2007.01383.x Environ Microbiol]<br />
# Yang C, Rodionov DA, Rodionova IA, Li X, Osterman AL. (2007) Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways., J Bacteriol. 2007 Dec 21; [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=18156253&cmd_current= PubMed] [http://jb.asm.org/cgi/reprint/JB.01469-07v1?view=long&pmid=18156253 JBact]<br />
# JR. Yates III and AL. Osterman (2007) Introduction: advances in genomics and proteomics. Chem Rev. Aug;107(8):3363-6. Epub 2007 Jul 21. [http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/cr068201u ACS]<br />
# DeJongh, M., Formsma, K., Boillot, P., Gould, J., Rycenga M., and Best, A. (2007) Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics 2007 [http://www.ncbi.nlm.nih.gov/pubmed/17462086 Pubmed] [http://www.biomedcentral.com/1471-2105/8/139 BMC Bioinformatics]<br />
<br />
=2008=<br />
# Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. BMC Genomics, 2008, The RAST Server: rapid annotations using subsystems technology. [http://www.ncbi.nlm.nih.gov/pubmed/18261238 Pubmed] [http://www.biomedcentral.com/1471-2164/9/75 BMC Genomics]<br />
<br />
=In press=<br />
# Desnues CG, B Rodriguez-Brito, S Rayhawk, S Kelley, T Tran, M Haynes, H Liu, D Hall, FE Angly, RA Edwards, RB Thurber, P Reid, J Siefert, V Souza, DL Valentine, BK Swan, M Breitbart, F Rohwer (2008; accepted) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature In press.<br />
# Mou, X.S., S., Edwards, R.A., Hodson, R.E. and Moran, M.A. (2007) Generalist Species Dominate Bacterial Carbon Processing in the Coastal Ocean. Nature, In Press.<br />
# Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut.</div>FolkerMeyer /w/index.php?title=Papers_that_use_the_SEED&diff=1801Papers that use the SEED2008-04-16T13:17:23Z<p>FolkerMeyer: </p>
<hr />
<div>=2005=<br />
# Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) Oct 7;33(17):5691-702. [http://www.ncbi.nlm.nih.gov/pubmed/16214803 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/33/17/5691 NAR] [http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplemental Online Material] <br />
=2006=<br />
# Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., Chan, A.M., Haynes, M., Kelley, S., Liu, H. et al. (2006) The marine viromes of four oceanic regions. PLoS Biol, 4. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=The%20marine%20viromes%20of%20four%20oceanic%20regions&cmd_current= PubMed] [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040368&ct=1 PLoS Biology]<br />
# DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., Martinez, A., Sullivan, M.B., Edwards, R., Brito, B.R. et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science, 311, 496-503. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=Community%20genomics%20among%20stratified%20microbial%20assemblages%20in%20the%20ocean%27s%20interior&cmd_current= PubMed]<br />
# Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander, E.C., Jr. and Rohwer, F. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 7, 57. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16549033&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/7/57 BioMed Central]<br />
# Gerdes, S., R. Edwards, M. Kubal, M. Fonstein, R. Stevens, and A. Osterman. (2006). Essential genes on metabolic maps. Curr Opin Biotechnol 17:448-56. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16978855 PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KWTFBB-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3067cb821f4b494047d5270860f5557c Science Direct]<br />
# Gerdes, S., Kurnasov, O., Shatalin, K., Polanuyer, B., Sloutsky, R., Vonstein, V., Overbeek, R., and A.L. Osterman (2006). Comparative Genomics of NAD Biosynthesis in Cyanobacteria. J. Bacteriol. 188: 3012-3023. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16585762&cmd_current= PubMed] [http://jb.asm.org/cgi/content/abstract/188/8/3012 J. Bact]<br />
# Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S., (2006). Experimental and computational assessment of conditionally essential genes in E. coli. J Bacteriol. 188(23):8259-71. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17012394 PubMed] [http://jb.asm.org/cgi/content/full/188/23/8259?view=long&pmid=17012394 JBact]<br />
# Krause, L., Diaz, N.N., Bartels, D., Edwards, R.A., Puhler, A., Rohwer, F., Meyer, F. and Stoye, J. (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22, e281. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16873483&cmd_current= PubMed] [http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e281 NAR]<br />
# Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162.<br />
# El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V. (2006) Discovery of a new prokaryotic type I GTP cyclohydrolase family. J Biol Chem. Dec 8;281(49):37586-93. Epub 2006 Oct 10. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17032654&cmd_current= PubMed] [http://www.jbc.org/cgi/content/full/281/49/37586 JBC]# Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, P., Jones, R., Robeson, M., Edwards, R., Felts, B., Rayhawk, S. et al. (2007) Metagenomic and small-subunit RNA surveys reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol, 73, 7059-7066. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17827313&cmd_current= PubMed] [http://aem.asm.org/cgi/content/full/73/21/7059?view=long&pmid=17827313 AEM]<br />
# Yang, C., D. A. Rodionov, X. Li, O. N. Laikova, M. S. Gelfand, O. P. Zagnitko, M. F. Romine, A. Y. Obraztsova, K. H. Nealson, and A. L. Osterman. (2006). Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem 281:29872-85. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16857666 PubMed] [http://www.jbc.org/cgi/content/full/281/40/29872 JBC]<br />
<br />
=2007=<br />
# de Crecy-Lagard V, Hanson AD. (2007) Finding novel metabolic genes through plant-prokaryote phylogenomics. Trends Microbiol. Dec;15(12):563-70. Epub 2007 Nov 9. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17997099&cmd_current= PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-4R3BW70-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=45c7be528111535816858125516a93ad Trends]<br />
# de Crecy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD. (2007) Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics. Jul 23;8:245.[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17645794&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/8/245 Biomed Central]<br />
# Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. (2007) Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation.Genome Res. Sep;17(9):1362-77. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17690205 PubMed] [http://www.genome.org/cgi/content/full/17/9/1362 Genome Research]<br />
# McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes SY, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman AL, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko OP, Xia F, Zinner J, Overbeek R, Stevens R.(2007) The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53 [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17145713 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D347 NAR]<br />
# Osterman, A., and T. Begley. (2007). A Subsystems-based approach to the identification of drug targets in bacterial pathogens, p. 132-170. In H.Boshoff and C.Barry (ed.), Progress in Drug Research, vol. 64. Birkhauser Verlag, Basel. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17195474 PubMed]<br />
# Dmitry A. Rodionov, Oleg V. Kurnasov, Boguslaw Stec, Yan Wang, Mary F. Roberts, and Andrei L. Osterman (2007) Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. . Proc Natl Acad Sci U S A. Mar 13;104(11):4279-84. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17360515 PubMed] [http://www.pnas.org/cgi/content/full/104/11/4279 PNAS]<br />
# Wegley, L., Breitbart, M., Edwards, R. and Rohwer, F. (2007) Functional and taxonimic analysis of coral-associated microbes using metagenomic analysis. Environ Microbiol, 9, 2707-2719. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17922755&cmd_current= PubMed] [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1462-2920.2007.01383.x Environ Microbiol]<br />
# Yang C, Rodionov DA, Rodionova IA, Li X, Osterman AL. (2007) Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways., J Bacteriol. 2007 Dec 21; [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=18156253&cmd_current= PubMed] [http://jb.asm.org/cgi/reprint/JB.01469-07v1?view=long&pmid=18156253 JBact]<br />
# JR. Yates III and AL. Osterman (2007) Introduction: advances in genomics and proteomics. Chem Rev. Aug;107(8):3363-6. Epub 2007 Jul 21. [http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/cr068201u ACS]<br />
# DeJongh, M., Formsma, K., Boillot, P., Gould, J., Rycenga M., and Best, A. (2007) Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics 2007 [http://www.ncbi.nlm.nih.gov/pubmed/17462086 Pubmed] [http://www.biomedcentral.com/1471-2105/8/139 BMC Bioinformatics]<br />
<br />
=2008=<br />
# Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. The RAST Server: rapid annotations using subsystems technology. [http://www.ncbi.nlm.nih.gov/pubmed/18261238 Pubmed] [http://www.biomedcentral.com/1471-2164/9/75 BMC Genomics]<br />
<br />
=In press=<br />
# Desnues CG, B Rodriguez-Brito, S Rayhawk, S Kelley, T Tran, M Haynes, H Liu, D Hall, FE Angly, RA Edwards, RB Thurber, P Reid, J Siefert, V Souza, DL Valentine, BK Swan, M Breitbart, F Rohwer (2008; accepted) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature In press.<br />
# Mou, X.S., S., Edwards, R.A., Hodson, R.E. and Moran, M.A. (2007) Generalist Species Dominate Bacterial Carbon Processing in the Coastal Ocean. Nature, In Press.<br />
# Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut.</div>FolkerMeyer /w/index.php?title=Papers_that_use_the_SEED&diff=1800Papers that use the SEED2008-04-16T13:12:20Z<p>FolkerMeyer: /* 2007 */</p>
<hr />
<div>=2005=<br />
# Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. (2005) Oct 7;33(17):5691-702. [http://www.ncbi.nlm.nih.gov/pubmed/16214803 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/33/17/5691 NAR] [http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplemental Online Material] <br />
=2006=<br />
# Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., Chan, A.M., Haynes, M., Kelley, S., Liu, H. et al. (2006) The marine viromes of four oceanic regions. PLoS Biol, 4. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=The%20marine%20viromes%20of%20four%20oceanic%20regions&cmd_current= PubMed] [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040368&ct=1 PLoS Biology]<br />
# DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.U., Martinez, A., Sullivan, M.B., Edwards, R., Brito, B.R. et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science, 311, 496-503. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=Community%20genomics%20among%20stratified%20microbial%20assemblages%20in%20the%20ocean%27s%20interior&cmd_current= PubMed]<br />
# Edwards, R.A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D.M., Saar, M.O., Alexander, S., Alexander, E.C., Jr. and Rohwer, F. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 7, 57. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16549033&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/7/57 BioMed Central]<br />
# Gerdes, S., R. Edwards, M. Kubal, M. Fonstein, R. Stevens, and A. Osterman. (2006). Essential genes on metabolic maps. Curr Opin Biotechnol 17:448-56. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16978855 PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KWTFBB-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3067cb821f4b494047d5270860f5557c Science Direct]<br />
# Gerdes, S., Kurnasov, O., Shatalin, K., Polanuyer, B., Sloutsky, R., Vonstein, V., Overbeek, R., and A.L. Osterman (2006). Comparative Genomics of NAD Biosynthesis in Cyanobacteria. J. Bacteriol. 188: 3012-3023. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16585762&cmd_current= PubMed] [http://jb.asm.org/cgi/content/abstract/188/8/3012 J. Bact]<br />
# Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S., (2006). Experimental and computational assessment of conditionally essential genes in E. coli. J Bacteriol. 188(23):8259-71. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17012394 PubMed] [http://jb.asm.org/cgi/content/full/188/23/8259?view=long&pmid=17012394 JBact]<br />
# Krause, L., Diaz, N.N., Bartels, D., Edwards, R.A., Puhler, A., Rohwer, F., Meyer, F. and Stoye, J. (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22, e281. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16873483&cmd_current= PubMed] [http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e281 NAR]<br />
# Rodriguez-Brito, B., Rohwer, F. and Edwards, R. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162.<br />
# El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V. (2006) Discovery of a new prokaryotic type I GTP cyclohydrolase family. J Biol Chem. Dec 8;281(49):37586-93. Epub 2006 Oct 10. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17032654&cmd_current= PubMed] [http://www.jbc.org/cgi/content/full/281/49/37586 JBC]# Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, P., Jones, R., Robeson, M., Edwards, R., Felts, B., Rayhawk, S. et al. (2007) Metagenomic and small-subunit RNA surveys reveal the high genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol, 73, 7059-7066. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17827313&cmd_current= PubMed] [http://aem.asm.org/cgi/content/full/73/21/7059?view=long&pmid=17827313 AEM]<br />
# Yang, C., D. A. Rodionov, X. Li, O. N. Laikova, M. S. Gelfand, O. P. Zagnitko, M. F. Romine, A. Y. Obraztsova, K. H. Nealson, and A. L. Osterman. (2006). Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem 281:29872-85. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=16857666 PubMed] [http://www.jbc.org/cgi/content/full/281/40/29872 JBC]<br />
<br />
=2007=<br />
# de Crecy-Lagard V, Hanson AD. (2007) Finding novel metabolic genes through plant-prokaryote phylogenomics. Trends Microbiol. Dec;15(12):563-70. Epub 2007 Nov 9. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17997099&cmd_current= PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-4R3BW70-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=45c7be528111535816858125516a93ad Trends]<br />
# de Crecy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD. (2007) Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics. Jul 23;8:245.[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17645794&cmd_current= PubMed] [http://www.biomedcentral.com/1471-2164/8/245 Biomed Central]<br />
# Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. (2007) Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation.Genome Res. Sep;17(9):1362-77. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17690205 PubMed] [http://www.genome.org/cgi/content/full/17/9/1362 Genome Research]<br />
# McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes SY, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman AL, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko OP, Xia F, Zinner J, Overbeek R, Stevens R.(2007) The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53 [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17145713 PubMed] [http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D347 NAR]<br />
# Osterman, A., and T. Begley. (2007). A Subsystems-based approach to the identification of drug targets in bacterial pathogens, p. 132-170. In H.Boshoff and C.Barry (ed.), Progress in Drug Research, vol. 64. Birkhauser Verlag, Basel. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17195474 PubMed]<br />
# Dmitry A. Rodionov, Oleg V. Kurnasov, Boguslaw Stec, Yan Wang, Mary F. Roberts, and Andrei L. Osterman (2007) Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. . Proc Natl Acad Sci U S A. Mar 13;104(11):4279-84. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17360515 PubMed] [http://www.pnas.org/cgi/content/full/104/11/4279 PNAS]<br />
# Wegley, L., Breitbart, M., Edwards, R. and Rohwer, F. (2007) Functional and taxonimic analysis of coral-associated microbes using metagenomic analysis. Environ Microbiol, 9, 2707-2719. [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=17922755&cmd_current= PubMed] [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1462-2920.2007.01383.x Environ Microbiol]<br />
# Yang C, Rodionov DA, Rodionova IA, Li X, Osterman AL. (2007) Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways., J Bacteriol. 2007 Dec 21; [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&orig_db=PubMed&term=18156253&cmd_current= PubMed] [http://jb.asm.org/cgi/reprint/JB.01469-07v1?view=long&pmid=18156253 JBact]<br />
# JR. Yates III and AL. Osterman (2007) Introduction: advances in genomics and proteomics. Chem Rev. Aug;107(8):3363-6. Epub 2007 Jul 21. [http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/cr068201u ACS]<br />
# DeJongh, M., Formsma, K., Boillot, P., Gould, J., Rycenga M., and Best, A. (2007) Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics 2007 [http://www.ncbi.nlm.nih.gov/pubmed/17462086 Pubmed] [http://www.biomedcentral.com/1471-2105/8/139 BMC Bioinformatics]<br />
<br />
=In press=<br />
# Desnues CG, B Rodriguez-Brito, S Rayhawk, S Kelley, T Tran, M Haynes, H Liu, D Hall, FE Angly, RA Edwards, RB Thurber, P Reid, J Siefert, V Souza, DL Valentine, BK Swan, M Breitbart, F Rohwer (2008; accepted) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature In press.<br />
# Mou, X.S., S., Edwards, R.A., Hodson, R.E. and Moran, M.A. (2007) Generalist Species Dominate Bacterial Carbon Processing in the Coastal Ocean. Nature, In Press.<br />
# Breitbart M, M Haynes, S Kelley, F Angly, R Edwards, B Felts, JM Mahaffy, J Mueller, J Nulton, S Rayhawk, B Rodriguez-Brito, P Salamon, F Rohwer (2008) Viral diversity and dynamics in an infant's gut.</div>FolkerMeyer /w/index.php?title=Home_of_the_SEED&diff=1791Home of the SEED2008-02-13T03:20:00Z<p>FolkerMeyer: </p>
<hr />
<div>With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. <br />
<br />
[[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]]<br />
<br />
Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology.<br />
<br />
<br />
Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. <br />
<br />
We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page.<br />
<br />
* We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material])<br />
* We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material])<br />
* Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]].<br />
* Other [[papers that use the SEED]]</div>FolkerMeyer /w/index.php?title=Home_of_the_SEED&diff=1789Home of the SEED2008-02-09T00:24:35Z<p>FolkerMeyer: </p>
<hr />
<div>With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. <br />
<br />
[[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]]<br />
<br />
Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology.<br />
<br />
<br />
Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. <br />
<br />
We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page.<br />
<br />
* We request that groups using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material])<br />
* We request that groups using the RAST server cite: Aziz et al., [http://www.biomedcentral.com/1471-2164/9/75| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material])<br />
* Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]].<br />
* Other [[papers that use the SEED]]</div>FolkerMeyer /w/index.php?title=Home_of_the_SEED&diff=1788Home of the SEED2008-01-31T17:57:35Z<p>FolkerMeyer: </p>
<hr />
<div>With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. <br />
<br />
[[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]]<br />
<br />
Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology.<br />
<br />
<br />
Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. <br />
<br />
We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page.<br />
<br />
* When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material])<br />
* Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]].<br />
* Other [[papers that use the SEED]]</div>FolkerMeyer /w/index.php?title=Home_of_the_SEED&diff=1787Home of the SEED2008-01-31T17:53:46Z<p>FolkerMeyer: </p>
<hr />
<div>With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. <br />
<br />
[[Image:Data_lifecycle3.png|frame|thumbnail|50px|Flow of data in the SEED.]]<br />
Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology.<br />
<br />
<br />
Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. <br />
<br />
We make all our software and data available for download via [ftp://ftp.theseed.org], also see our [[DownloadPage]] page.<br />
<br />
* When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material])<br />
* Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]].<br />
* Other [[papers that use the SEED]]</div>FolkerMeyer /w/index.php?title=File:Data_lifecycle3.png&diff=1786File:Data lifecycle3.png2008-01-31T17:52:22Z<p>FolkerMeyer: </p>
<hr />
<div></div>FolkerMeyer /w/index.php?title=Home_of_the_SEED&diff=1785Home of the SEED2008-01-31T17:49:17Z<p>FolkerMeyer: </p>
<hr />
<div>With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the [http://thefig.info Fellowship for Interpretation of Genomes (FIG)] as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data. <br />
<br />
[[Image:Data_lifecycle2.png|right|150p|Flow of data in the SEED.]]<br />
Curation of genomic data ([[Glossary#Annotation|annotation]]) is done via the curation of [[Glossary#Subsystem|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([[Glossary#FIGfam|FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology.<br />
<br />
<br />
Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free [http://rast.nmpdr.org RAST-Server] (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the [http://metagenomics.nmpdr.org Metagenomics-RAST-Server] freely available. We also provide a [http://seed-viewer.theseed.org/ SEED-Viewer] that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the [http://theseed.uchicago.edu/FIG/index.cgi Trial-SEED]. <br />
<br />
We make all our software and data available for download via [ftp://ftp.theseed.org] , also see our [[DownloadPage]] page.<br />
<br />
* When using the SEED, please cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Acids Res 33(17)], 2005 ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material])<br />
* Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]].<br />
* Other [[papers that use the SEED]]</div>FolkerMeyer /w/index.php?title=File:Data_lifecycle2.png&diff=1784File:Data lifecycle2.png2008-01-31T17:40:38Z<p>FolkerMeyer: </p>
<hr />
<div></div>FolkerMeyer /w/index.php?title=File:Cycle_diagram.png&diff=1783File:Cycle diagram.png2008-01-31T15:50:36Z<p>FolkerMeyer: Flow of annotations from Subsystem based curation into FIGfams and the subsequent use of those in the RAST server.</p>
<hr />
<div>Flow of annotations from Subsystem based curation into FIGfams and the subsequent use of those in the RAST server.</div>FolkerMeyer /w/index.php?title=Glossary&diff=1757Glossary2007-12-09T00:57:42Z<p>FolkerMeyer: </p>
<hr />
<div>=== Annotators SEED ===<br />
The master copy for all data in the SEED environment. Users can not access this password protected site.<br />
All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]].<br />
<br />
=== Annotation ===<br />
please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]]<br />
<br />
=== Assigning a gene function and annotation ===<br />
Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. <br />
<br />
We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. <br />
<br />
=== Assignment ===<br />
please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]]<br />
<br />
=== Bidirectional Best Hit (BBH) ===<br />
<br />
The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling]<br />
defines a Bidirectional Best Hit or BBH as follows:<br />
<br />
<blockquote><br />
Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required fasta3 scores lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb. Genes (Xa, Ya) from Ga and (Xb, Yb) from Gb form a “pair of close bidirectional best hits (PCBBH)” if and only if Xa and Ya are close, Xb and Yb are close, Xa and Xb are a BBH, and Ya and Yb are a BBH.<br />
</blockquote><br />
<br />
=== Clearinghouse ===<br />
please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]]<br />
<br />
===Feature===<br />
A feature is a defined region in the DNA. A PEG is the most prevalent feature type in the SEED. Some other feature types include<br />
RNA, prophage and pathogenicity islands. The format for a feature ID is fig|genome_id.feature_abbreviation.feature_number (ie fig|83333.1.peg.100 ). <br />
<br />
=== FIGfam ===<br />
FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows:<br />
<br />
# Two PEGs which both occur within a single FIGfam are believed to have the same function.<br />
<br />
# There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family.<br />
<br />
=== FIG Identifier / FIG-IDs ===<br />
We provide identifiers for genome sequences and features in the following form:<br />
<br />
{|<br />
! Entity type !! key !! identifier<br />
|-<br />
| Genome || genome || fig<nowiki>|</nowiki>83331.1 <br />
|-<br />
| PEG || id || fig<nowiki>|</nowiki>83331.peg.123 <br />
|-<br />
| RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 <br />
|-<br />
|}<br />
<br />
(Please also see below for information on how to link to the SEED.)<br />
<br />
=== Functional role ===<br />
The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell.<br />
<br />
=== Gene function ===<br />
The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in <br />
<br />
http://www.nmpdr.org/FIG/Html/SEED_functions.html<br />
<br />
Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. <br />
<br />
=== Linking to the SEED ===<br />
<br />
We support linking to the SEED using a generic mechanism:<br />
<br />
Base URL: <br />
<br />
http://www.theseed.org/linkin.cgi?<br />
<br />
{|<br />
|+ Supported SEED Identifiers for external use<br />
! Entity type !! key !! identifier !! Example<br />
|-<br />
| Genome || genome || fig<nowiki>|</nowiki>83331.1 || [[http://www.theseed.org/linkin.cgi?genome=fig|83333.1 http://www.theseed.org/linkin.cgi?genome=fig&#124;83333.1]]<br />
|-<br />
| PEG || id || fig<nowiki>|</nowiki>83331.peg.123 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.peg.123 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.peg.123]]<br />
|-<br />
| RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.rna.1 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.rna.1]]<br />
|-<br />
|}<br />
<br />
SEED identifiers contain the NCBI taxonomy ID, thus if the taxonomy ID changes, we need to update our internal data accordingly. To provide stable external identifiers, we keep a list of IDs that have changed and display warning message informing the user of the change and provide a link to the new version of the data requested.<br />
<br />
=== Metabolic Reconstruction ===<br />
When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems.<br />
<br />
=== NMPDR pathogen genome === <br />
<br />
The NMPDR is responsible for five classes of genomes:<br />
<br />
# Campylobacter jejuni<br />
# Listeria monocytogenes<br />
# Staphylococcus aureus<br />
# Streptococcus pneumoniae and Streptococcus pyogenes<br />
# Pathogenic Vibrio<br />
<br />
=== Pair of Close Homologs (PCH) ===<br />
<br />
The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling]<br />
defines a Pair of Close Homologs as follows:<br />
<br />
<blockquote><br />
We can also define the concept of “pairs of close homologs” (PCHs) as follows: genes (X′a, Y′a) from Ga and (X′b, Y′b) from Gb form a PCH if and only if X′a and Y′a are close, X′b and Y′b are close, X′a and X′b are recognizably similar, and Y′a and Y′b are recognizably similar. Here, we will consider two genes to be recognizably similar if their gene products produce fasta3 scores lower than 1.0 × 10−5. We use a scoring scheme analogous to the one described for PCBBHs to evaluate the connections between PCHs, except that if Ga and Gb are the same genome, we assign an arbitrary “same-genome score” (“same-genome” pairs cannot occur for PCBBHs by definition, but for PCHs they are possible). Unlike PCBBHs from two very close genomes for which contiguity is completely uninformative in the vast majority of cases, PCHs allow recognition of gene clusters that play similar (but usually not identical) roles (such as two transport cassettes containing pairs of homologs) in the same or similar organisms. The arbitrary “same-genome score” should, we believe, have a value that is high enough to rank such instances as significant. <br />
</blockquote><br />
<br />
=== PEG ===<br />
A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence).<br />
<br />
=== Populated Subsystem ===<br />
please see [[#Subsystem|Subsystem]]<br />
<br />
<br />
=== RAST ===<br />
RAST or Rapid Annotation using Subsystem Technology is a rapid and very accurate annotation technology. We make a RAST server available for public use at <br />
<br />
http://rast.nmpdr.org<br />
<br />
=== SEED-Viewer ===<br />
The SEED Viewer is a web-based application that allows browsing of SEED data structures.<br />
<br />
We use the SEED-Viewer to provide a public read-only version of the latest SEED data at:<br />
<br />
http://seed-viewer.theseed.org<br />
<br />
'''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version.<br />
<br />
=== Subsystem ===<br />
A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of <br />
[[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts.<br />
<br />
=== Subsystem Clearing House ===<br />
Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via <br />
http://clearinghouse.theseed.org/clearinghouse_browser.cgi? <br />
<br />
=== Trial-SEED ===<br />
A public, read-write copy of the SEED is made available on <br />
<br />
http://theseed.uchicago.edu/FIG/index.cgi<br />
<br />
'''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]].<br />
<br />
=== Variant Code===<br />
please see [[#Subsystem|Subsystem]]</div>FolkerMeyer /w/index.php?title=Glossary&diff=1756Glossary2007-12-09T00:57:14Z<p>FolkerMeyer: </p>
<hr />
<div>=== Annotators SEED ===<br />
The master copy for all data in the SEED environment. Users can not access this password protected site.<br />
All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]].<br />
<br />
=== Annotation ===<br />
please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]]<br />
<br />
=== Assigning a gene function and annotation ===<br />
Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. <br />
<br />
We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. <br />
<br />
=== Assignment ===<br />
please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]]<br />
<br />
=== Bidirectional Best Hit (BBH) ===<br />
<br />
The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling]<br />
defines a Bidirectional Best Hit or BBH as follows:<br />
<br />
<blockquote><br />
Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required fasta3 scores lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb. Genes (Xa, Ya) from Ga and (Xb, Yb) from Gb form a “pair of close bidirectional best hits (PCBBH)” if and only if Xa and Ya are close, Xb and Yb are close, Xa and Xb are a BBH, and Ya and Yb are a BBH.<br />
</blockquote><br />
<br />
=== Clearinghouse ===<br />
please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]]<br />
<br />
===Feature===<br />
A feature is a defined region in the DNA. A PEG is the most prevalent feature type in the SEED. Some other feature types include<br />
RNA, prophage and pathogenicity islands. The format for a feature ID is fig|genome_id.feature_abbreviation.feature_number (ie fig|83333.1.peg.100 ). <br />
<br />
=== FIGfam ===<br />
FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows:<br />
<br />
# Two PEGs which both occur within a single FIGfam are believed to have the same function.<br />
<br />
# There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family.<br />
<br />
=== FIG Identifier / FIG-IDs ===<br />
We provide identifiers for genome sequences and features in the following form:<br />
<br />
{|<br />
! Entity type !! key !! identifier<br />
|-<br />
| Genome || genome || fig<nowiki>|</nowiki>83331.1 <br />
|-<br />
| PEG || id || fig<nowiki>|</nowiki>83331.peg.123 <br />
|-<br />
| RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 <br />
|-<br />
|}<br />
<br />
(Please also see below for information on how to link to the SEED.)<br />
<br />
=== Functional role ===<br />
The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell.<br />
<br />
=== Gene function ===<br />
The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in <br />
<br />
http://www.nmpdr.org/FIG/Html/SEED_functions.html<br />
<br />
Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. <br />
<br />
=== Linking to the SEED ===<br />
<br />
We support linking to the SEED using a generic mechanism:<br />
<br />
Base URL: <br />
<br />
http://www.theseed.org/linkin.cgi?<br />
<br />
{|<br />
|+ Supported SEED Identifiers for external use<br />
! Entity type !! key !! identifier !! Example<br />
|-<br />
| Genome || genome || fig<nowiki>|</nowiki>83331.1 || [[http://www.theseed.org/linkin.cgi?genome=fig|83333.1 http://www.theseed.org/linkin.cgi?genome=fig&#124;83333.1]]<br />
|-<br />
| PEG || id || fig<nowiki>|</nowiki>83331.peg.123 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.peg.123 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.peg.123]]<br />
|-<br />
| RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.rna.1 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.rna.1]]<br />
|-<br />
|}<br />
<br />
SEED identifiers contain the NCBI taxonomy ID, thus if the taxonomy ID changes, we need to update our internal data accordingly. To provide stable external identifiers, we keep a list of IDs that have changed and display warning message informing the user of the change and provide a link to the new version of the data requested.<br />
<br />
=== Metabolic Reconstruction ===<br />
When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems.<br />
<br />
=== NMPDR pathogen genome === <br />
<br />
The NMPDR is responsible for five classes of genomes:<br />
<br />
# Campylobacter jejuni<br />
# Listeria monocytogenes<br />
# Staphylococcus aureus<br />
# Streptococcus pneumoniae and Streptococcus pyogenes<br />
# Pathogenic Vibrio<br />
<br />
=== Pair of Close Homologs (PCH) ===<br />
<br />
The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling]<br />
defines a Pair of Close Homologs as follows:<br />
<br />
<blockquote><br />
We can also define the concept of “pairs of close homologs” (PCHs) as follows: genes (X′a, Y′a) from Ga and (X′b, Y′b) from Gb form a PCH if and only if X′a and Y′a are close, X′b and Y′b are close, X′a and X′b are recognizably similar, and Y′a and Y′b are recognizably similar. Here, we will consider two genes to be recognizably similar if their gene products produce fasta3 scores lower than 1.0 × 10−5. We use a scoring scheme analogous to the one described for PCBBHs to evaluate the connections between PCHs, except that if Ga and Gb are the same genome, we assign an arbitrary “same-genome score” (“same-genome” pairs cannot occur for PCBBHs by definition, but for PCHs they are possible). Unlike PCBBHs from two very close genomes for which contiguity is completely uninformative in the vast majority of cases, PCHs allow recognition of gene clusters that play similar (but usually not identical) roles (such as two transport cassettes containing pairs of homologs) in the same or similar organisms. The arbitrary “same-genome score” should, we believe, have a value that is high enough to rank such instances as significant. <br />
</blockquote><br />
<br />
=== PEG ===<br />
A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence).<br />
<br />
=== Populated Subsystem ===<br />
please see [[#Subsystem|Subsystem]]<br />
<br />
<br />
=== RAST ===<br />
RAST or Rapid Annotation using Subsystem Technology is a rapid and very accurate annotation technology. We make a RAST server available for public use at [[http://rast.nmpdr.org]]<br />
<br />
=== SEED-Viewer ===<br />
The SEED Viewer is a web-based application that allows browsing of SEED data structures.<br />
<br />
We use the SEED-Viewer to provide a public read-only version of the latest SEED data at:<br />
<br />
http://seed-viewer.theseed.org<br />
<br />
'''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version.<br />
<br />
=== Subsystem ===<br />
A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of <br />
[[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts.<br />
<br />
=== Subsystem Clearing House ===<br />
Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via <br />
http://clearinghouse.theseed.org/clearinghouse_browser.cgi? <br />
<br />
=== Trial-SEED ===<br />
A public, read-write copy of the SEED is made available on <br />
<br />
http://theseed.uchicago.edu/FIG/index.cgi<br />
<br />
'''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]].<br />
<br />
=== Variant Code===<br />
please see [[#Subsystem|Subsystem]]</div>FolkerMeyer /w/index.php?title=Glossary&diff=1755Glossary2007-12-09T00:55:19Z<p>FolkerMeyer: </p>
<hr />
<div>=== Annotators SEED ===<br />
The master copy for all data in the SEED environment. Users can not access this password protected site.<br />
All annotations are made available via the [[#SEED-Viewer| SEED-Viewer]] and the [[#Trial-SEED|Trial-SEED]].<br />
<br />
=== Annotation ===<br />
please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]]<br />
<br />
=== Assigning a gene function and annotation ===<br />
Annotators assign gene functions to genes, and we call this process annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our annotators to annotate the genes included in a [[#subsystem|Subsystem]] (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our annotators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes. <br />
<br />
We use the term annotation to refer to assigning functions to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity certainly is closely related to the construction of subsystems and protein families (which we call FIGfams), but we will describe those activities elsewhere. <br />
<br />
=== Assignment ===<br />
please see [[#Assigning_a_gene_function_and_annotation| Assigning a gene function and annotation]]<br />
<br />
=== Bidirectional Best Hit (BBH) ===<br />
<br />
The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling]<br />
defines a Bidirectional Best Hit or BBH as follows:<br />
<br />
<blockquote><br />
Given two genes Xa and Xb from two genomes Ga and Gb, Xa and Xb are called a “bidirectional best hit (BBH)” if and only if recognizable similarity exists between them (in our case, we required fasta3 scores lower than 1.0 × 10−5), there is no gene Zb in Gb that is more similar than Xb is to Xa, and there is no gene Za in Ga that is more similar than Xa is to Xb. Genes (Xa, Ya) from Ga and (Xb, Yb) from Gb form a “pair of close bidirectional best hits (PCBBH)” if and only if Xa and Ya are close, Xb and Yb are close, Xa and Xb are a BBH, and Ya and Yb are a BBH.<br />
</blockquote><br />
<br />
=== Clearinghouse ===<br />
please see [[#SubsystemClearinghouse|Subsystem Clearinghouse]]<br />
<br />
===Feature===<br />
A feature is a defined region in the DNA. A PEG is the most prevalent feature type in the SEED. Some other feature types include<br />
RNA, prophage and pathogenicity islands. The format for a feature ID is fig|genome_id.feature_abbreviation.feature_number (ie fig|83333.1.peg.100 ). <br />
<br />
=== FIGfam ===<br />
FIGfams are protein families generated by the Fellowship for Interpretation of Genomes (FIG). These families are based on the collection of subsystems, as well as correspondences between genes in closely related strains (we describe the construction of FIGfams in a separate SOP). The important properties of these families are as follows:<br />
<br />
# Two PEGs which both occur within a single FIGfam are believed to have the same function.<br />
<br />
# There is a decision procedure associated with the family which can be invoked to determine whether or not a gene can be “safely” assigned the function associated with the family.<br />
<br />
=== FIG Identifier / FIG-IDs ===<br />
We provide identifiers for genome sequences and features in the following form:<br />
<br />
{|<br />
! Entity type !! key !! identifier<br />
|-<br />
| Genome || genome || fig<nowiki>|</nowiki>83331.1 <br />
|-<br />
| PEG || id || fig<nowiki>|</nowiki>83331.peg.123 <br />
|-<br />
| RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 <br />
|-<br />
|}<br />
<br />
(Please also see below for information on how to link to the SEED.)<br />
<br />
=== Functional role ===<br />
The concept of functional role is both basic and primitive in the sense that we will not pretend to offer a precise definition. It corresponds roughly to a single logical role that a gene or gene product may play in the operation of a cell.<br />
<br />
=== Gene function ===<br />
The function of a protein-encoding gene (PEG) is the functional role played by the product of the gene or an expression describing a set of roles played by the encoded protein. The operators used to construct expressions and the meanings associated with the operators are described in <br />
<br />
http://www.nmpdr.org/FIG/Html/SEED_functions.html<br />
<br />
Genes other than PEGs can also be assigned functions (e.g., SSU rRNA). However, in most cases the functions assigned to genes other than PEGs tend not to be problematic. <br />
<br />
=== Linking to the SEED ===<br />
<br />
We support linking to the SEED using a generic mechanism:<br />
<br />
Base URL: <br />
<br />
http://www.theseed.org/linkin.cgi?<br />
<br />
{|<br />
|+ Supported SEED Identifiers for external use<br />
! Entity type !! key !! identifier !! Example<br />
|-<br />
| Genome || genome || fig<nowiki>|</nowiki>83331.1 || [[http://www.theseed.org/linkin.cgi?genome=fig|83333.1 http://www.theseed.org/linkin.cgi?genome=fig&#124;83333.1]]<br />
|-<br />
| PEG || id || fig<nowiki>|</nowiki>83331.peg.123 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.peg.123 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.peg.123]]<br />
|-<br />
| RNA feature || id || fig<nowiki>|</nowiki>83331.rna.1 || [[http://www.theseed.org/linkin.cgi?id=fig|83333.1.rna.1 http://www.theseed.org/linkin.cgi?id=fig&#124;83333.1.rna.1]]<br />
|-<br />
|}<br />
<br />
SEED identifiers contain the NCBI taxonomy ID, thus if the taxonomy ID changes, we need to update our internal data accordingly. To provide stable external identifiers, we keep a list of IDs that have changed and display warning message informing the user of the change and provide a link to the new version of the data requested.<br />
<br />
=== Metabolic Reconstruction ===<br />
When we use the term metabolic reconstruction of a given genome we will simply mean the set of populated subsystems that contain the genome, the PEGs (and their assigned functions) that are connected to functional roles in these populated subsystems, and the specific variant code associated with the genome in each of the populated subsystems.<br />
<br />
=== NMPDR pathogen genome === <br />
<br />
The NMPDR is responsible for five classes of genomes:<br />
<br />
# Campylobacter jejuni<br />
# Listeria monocytogenes<br />
# Staphylococcus aureus<br />
# Streptococcus pneumoniae and Streptococcus pyogenes<br />
# Pathogenic Vibrio<br />
<br />
=== Pair of Close Homologs (PCH) ===<br />
<br />
The paper [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=10077608 The use of gene clusters to infer functional coupling]<br />
defines a Pair of Close Homologs as follows:<br />
<br />
<blockquote><br />
We can also define the concept of “pairs of close homologs” (PCHs) as follows: genes (X′a, Y′a) from Ga and (X′b, Y′b) from Gb form a PCH if and only if X′a and Y′a are close, X′b and Y′b are close, X′a and X′b are recognizably similar, and Y′a and Y′b are recognizably similar. Here, we will consider two genes to be recognizably similar if their gene products produce fasta3 scores lower than 1.0 × 10−5. We use a scoring scheme analogous to the one described for PCBBHs to evaluate the connections between PCHs, except that if Ga and Gb are the same genome, we assign an arbitrary “same-genome score” (“same-genome” pairs cannot occur for PCBBHs by definition, but for PCHs they are possible). Unlike PCBBHs from two very close genomes for which contiguity is completely uninformative in the vast majority of cases, PCHs allow recognition of gene clusters that play similar (but usually not identical) roles (such as two transport cassettes containing pairs of homologs) in the same or similar organisms. The arbitrary “same-genome score” should, we believe, have a value that is high enough to rank such instances as significant. <br />
</blockquote><br />
<br />
=== PEG ===<br />
A Protein Encoding Gene (PEG) is equivalent to a CDS (Coding Sequence).<br />
<br />
=== Populated Subsystem ===<br />
please see [[#Subsystem|Subsystem]]<br />
<br />
=== SEED-Viewer ===<br />
The SEED Viewer is a web-based application that allows browsing of SEED data structures.<br />
<br />
We use the SEED-Viewer to provide a public read-only version of the latest SEED data at:<br />
<br />
http://seed-viewer.theseed.org<br />
<br />
'''Please note''': The data is updated automatically every 24 hours. When citing or linking to the SEED please use this version.<br />
<br />
=== Subsystem ===<br />
A subsystem is a set of functional roles that an annotator has decided should be thought of as related. Frequently, subsystems represent the collection of <br />
[[#Functional_role|functional roles]] that make up a metabolic pathway, a complex (e.g., the ribosome), or a class of proteins (e.g., two-component signal-transduction proteins within Staphylococcus aureus). A '''populated subsystem''' is a subsystem with an attached spreadsheet. The rows of the spreadsheet represent genomes and the columns represent the functional roles of the spreadsheet. Each cell contains the identifiers of genes from the corresponding genome the implement the specific functional role. That is, a populated subsystem specifies which genes implement instances of the subsystem in each of the genomes. The rows of a populated genome are assigned '''variant codes''' which describe which of a set of possible variants of the subsystem exist within each genome (special codes expressing a total absence of the subsystem or remaining uncertainty exist). Construction of a large set of curated populated subsystems is at the center of the NMPDR and SEED annotation efforts.<br />
<br />
=== Subsystem Clearing House ===<br />
Since annotators can work on any machine (including the public SEED) the way to propagate subsystems is via <br />
http://clearinghouse.theseed.org/clearinghouse_browser.cgi? <br />
<br />
=== Trial-SEED ===<br />
A public, read-write copy of the SEED is made available on <br />
<br />
http://theseed.uchicago.edu/FIG/index.cgi<br />
<br />
'''Please note''': The data on this server is updated in irregular intervals. Users should not assume that annotations made on this system will persist. Please publish your annotations to the [[#Subsystem_clearing_house|Subsystem Clearing house]].<br />
<br />
=== Variant Code===<br />
please see [[#Subsystem|Subsystem]]</div>FolkerMeyer