TheSeed - User contributions [en]

SpecialPurposeDBs

2009-01-06T15:39:21Z

Marland:

== EGGS database: Essential Genes on Genome Scale ==

SEED maintains an up-to-date database of all microbial gene essentiality data experimentally obtained in the currently published genome-scale gene essentiality screens (listed in Table 1). Comparative analysis of these data across multiple organisms in a rich genomic, biochemical, and phylogenetic contexts provided by the collection of annotated Subsystems greatly facilitates their interpretation and practical applications, such as, understanding of cellular networks, gene and pathway discovery, identification of novel drug targets, and strain engineering.

[http://www.nmpdr.org/FIG/wiki/view.cgi/Main/EssentialGenes EGGS Database]

MediaWiki:Sidebar

2009-01-06T14:01:24Z

Marland:

SEED People

2008-12-18T20:59:18Z

Marland:

The people behind SEED are the following:

* [http://www.thefig.info '''FIG''']
** Ross Overbeek
** Veronika Vonstein
** Gordon Pusch
** Bruce Parrello
** Rob Edwards
** Andrei Osterman
** Michael Fonstein
** Svetlana Gerdes
** Olga Zagnitko
** Olga Vassieva
** Yakov Kogan
** Irina Goltsman

* [http://www.mcs.anl.gov '''Mathematics and Computer Science Department'''] [http://www.anl.gov '''Argonne National Labs''']
** Rick Stevens
** Terry Disz
** Robert Olson
** Folker Meyer
** Elizabeth Glass
** Chris Henry
** Jared Wilkening

* [http://www.ci.uchicago.ed '''Computation Institute'''] [http://www.uchicago.edu '''University of Chicago''']
** Daniela Bartels
** Michael Kubal
** William Mihalo
** Tobias Paczian
** Andreas Wilke
** Alex Rodriguez
** Mark D'Souza

* [http://www.uiuc.edu '''University of Illinois at Urbana-Champaign''']
** Gary J. Olson
** Leslie McNeil
** Claudia Reich

* [http://www.hope.edu '''Hope College''']
** Matt DeJongh
** Aaron Best

* [http://www.utmem.edu/ '''University of Memphis Tennessee''']
** Rami Aziz

* '''Alumni'''
** Daniel Paarmann
** Jen Zinner
** Matt Cohoon

Video Tutorials

2008-12-18T18:59:53Z

Marland:

'''RAST Sever Video Tutorials'''

Coming soon ...

SEED People

2008-12-18T18:56:30Z

Marland:

The people behind SEED are the following:

* [http://www.thefig.info '''FIG''']
** Ross Overbeek
** Veronika Vonstein
** Gordon Pusch
** Bruce Parrello
** Rob Edwards
** Andrei Osterman
** Michael Fonstein
** Svetlana Gerdes
** Olga Zagnitko
** Olga Vassieva
** Yakov Kogan
** Irina Goltsman

* [http://www.mcs.anl.gov '''Mathematics and Computer Science Department'''] [http://www.anl.gov '''Argonne National Labs''']
** Rick Stevens
** Terry Disz
** Robert Olson
** Folker Meyer
** Elizabeth Glass
** Chris Henry

* [http://www.ci.uchicago.ed '''Computation Institute'''] [http://www.uchicago.edu '''University of Chicago''']
** Daniela Bartels
** Matt Cohoon
** Michael Kubal
** William Mihalo
** Tobias Paczian
** Andreas Wilke
** Jen Zinner
** Alex Rodriguez
** Mark D'Souza
** Jared Wilkening

* [http://www.uiuc.edu '''University of Illinois at Urbana-Champaign''']
** Gary J. Olson
** Leslie McNeil

* [http://www.hope.edu '''Hope College''']
** Matt DeJongh
** Aaron Best

* [http://www.utmem.edu/ '''University of Memphis Tennessee''']
** Rami Aziz

* '''Alumni'''
** Daniel Paarmann

SEED People

2008-12-18T18:53:59Z

Marland:

The people behind SEED are the following:

* [http://www.thefig.info FIG]
** Ross Overbeek
** Veronika Vonstein
** Gordon Pusch
** Bruce Parrello
** Rob Edwards
** Andrei Osterman
** Michael Fonstein
** Svetlana Gerdes
** Olga Zagnitko
** Olga Vassieva
** Yakov Kogan
** Irina Goltsman

* [http://www.mcs.anl.gov Mathematics and Computer Science Department] [http://www.anl.gov Argonne National Labs]
** Rick Stevens
** Terry Disz
** Robert Olson
** Folker Meyer
** Elizabeth Glass
** Chris Henry

* [http://www.ci.uchicago.ed Computation Institute] [http://www.uchicago.edu University of Chicago]
** Daniela Bartels
** Matt Cohoon
** Michael Kubal
** William Mihalo
** Tobias Paczian
** Andreas Wilke
** Jen Zinner
** Alex Rodriguez
** Mark D'Souza
** Jared Wilkening

* [http://www.uiuc.edu University of Illinois at Urbana-Champaign]
** Gary J. Olson
** Leslie McNeil

* [http://www.hope.edu Hope College]
** Matt DeJongh
** Aaron Best

* [http://www.utmem.edu/ University of Memphis Tennessee]
** Rami Aziz

Alumni
** Daniel Paarmann

Contact

2008-12-18T18:50:10Z

Marland:

Have questions or comments about our applications?

'''NMPDR'''

Email: [mailto:help@nmpdr.org]

Bugs: [mailto:bugs@nmpdr.org]

'''RAST'''

Email: [mailto:rast@mcs.anl.gov]

'''Metagenomics RAST'''

Email: [mailto:mg-rast@mcs.anl.gov]

'''The SEED'''

Email: [mailto:info@theseed.org]

MG RAST v2.0 tutorial

2008-09-08T22:03:11Z

Marland:

== '''MG-RAST Tutorial''' ==

Start Page
The start page of MG-RAST provides users with access to registration, data submission and management tools for uploaded data. Access to public genomes is also available once you login. Only once you have logged in and have selected a metagenome, can you gain access to your jobs, view your results and use comparative tools.

'''Registration'''

Registering for the first time? → Choose '''New Account'''. Please enter your first and last name as well as your email address into the registration form. Then please select your country and choose a login name. It's recommended to use only letters and digits for your login name, without spaces. You will then shortly receive an email with more information about the registration.

Already have an account for one of our other services? → Choose Existing Account. Please enter your login and email of that account. If your group administrator has given you a group name, please enter it in the group name field, otherwise leave this field blank.

'''Upload a Genome/Creating a Job'''

Uploading your metagenome has a few steps. The first is uploading your fasta file. File requirements and suggestions:

• The fasta file name must end in .fa, .fasta, .fas, .fsa, or .fna.

• Files larger than 30 MB should compress (.tgz) their file or contact us for other options.

• Quality files (.qual) may also be included along with the sequence file for submission to MG-RAST. The quality file should be combines into a single archive (that ends in .tgz) and then uploaded to the server.

How to I create a .tgz file?
Example: create the file metagenome.tar.gz from two fna files.
tar -cvzf metagenome.tar.gz seqfile1.fna seqfile2.fna

The second step requires that you provide a project name, a name for your metagenome and a brief description of the sample. The second tab shows an Upload Summary of the number of files uploaded for submission.

The third and last step asks for users to supply information about the metagenome sample. These description fields were adopted from MIGs (Minimum Information about a Genome Sequence) specification. You can also elect to make your metagenome publicly available, this option is also available if you wish to do so at a later date. During this step you also have the option of removing duplicate sequences from the analysis.

'''Jobs Overview'''

The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and all that are public. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress.

The table of jobs can be sorted on Job ID or searchable (text boxes in header row). This is especially useful when the user has numerous metagenomes to select from.

Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found.
'''
Job Details'''

Here you are able to:

• Share with selected users by providing their email addresses.

• Make the metagenome publicly accessible

• View detailed information on the processing of your job.

• View your results!!

• Download your results!!

'''Overview'''

The overview page has several sections, the first being the overall statistics of your sample. How these numbers were calculated can be found here (http://www.theseed.org/wiki/MG-RAST_Numbers). The second section is a summary table of taxonomic distribution based on best protein similarity to SEED and 16S based similarity to RDP. The third section is the statistical summary in paragraph form along with graphical representations of sequence length and GC distributions. The last section outlines the metagenome description and MIGS data you submitted along with your sequence file.

The navigation bar has new options not previously seen on the start page or job management pages. Now you have access to tools that will allow you to compare your metagenome to other metagenomes in regard to metabolism and phylogeny (Fragment Profile). Also available is metabolic comparisons against bacterial genomes (also known as a recruitment plot).
'''
Fragment Profile'''

To view your metabolic or phylogenetic profiles, first select the category. Once a category is selected you can then choose your dataset in which to based you profile. For metabolic reconstructions the Subsystem dataset is available. For phylogeny, RDP, Silva, European Ribosomal and GREENGENES are all options. Parameters are also changeable; users can change e-value, p-value, percent identity, and minimum alignment length. This will allow you to refine the analysis to suit the sequence characteristics of your sample. We recommend a minimal alignment length of 50bp be used with all RNA databases.

* Note: Metabolic reconstructions are based on SEED functional roles and Subsystems. (There is also a tool to view this via KEGG maps and do comparisons by going to the “Compare Metagenomes” link in the navigation bar.)

Profile results are presented in two ways: Pie chart and table. Phylogeny and Metabolism are hierarchical and the pie charts reflect that notion. By clicking on a section of the pie chart, an additional chart appears detailing the breakdown of that group. This is possible down to a third level. All selections made to the chart are reflected in the accompanying table (second tab). The numbers shown in the chart and table are actual counts.

'''Compare Metagenome to other Metagenomes - Heat Maps'''

You can compare the metabolism or phylogeny of your metagenome with one more other metagenomes. Just as was seen looking at the Fragment Profile, you can select your database and modify your parameters. For metabolic reconstructions the Subsystem dataset is available. For phylogeny, RDP, Silva, European Ribosomal and GREENGENES are all options. Parameters are also changeable; users can change e-value, p-value, percent identity, and minimum alignment length. This will allow you to refine the analysis to suit the sequence characteristics of your sample. We recommend a minimal alignment length of 50bp be used with all RNA databases.
The Heat Maps show the relative abundance, which is calculated using the number of sequences in a subsystem/tax class as a fraction of the total number of sequences in a subsystem/dataset. This allows for correction based on the sample size.

'''Compare Metagenome to Organism - Recruitment Plot'''

You can compare metabolism of your sample with the metabolic reconstructions from bacterial genomes. Choosing an organism predicted in your sample, you can compare the metabolic coverage. Like most of the comparative tools in MG-RAST you can modify the parameters of the calculated Metabolic Reconstruction including e-value, p-value , percent identity and minimum alignment length.

'''Compare Metagenome – KEGG Map
'''
MG-RAST also enables users to view their sample on KEGG maps and compare with others. Mapping of functional roles to KEGG maps was done using functional assignments from analysis against the SEED. Absolute counts are provided for each KEGG map. These maps are hierarchical, just like the Subsystems, which allow you to browse the sample on various levels or compare it with other metagenomes.

RAST Quality Report

2008-02-15T14:35:10Z

Marland:

The RAST Server offers a brief quality report on the [[RAST_Tutorial#Jobs_Overview|Job Details]] of your genome. The purpose of this page is to explain what those statistics mean and how we compute them.

For those explanations, PEG refers to protein encoding gene and is equivalent to a CDS (Coding Sequence).

== Summary ==

'''Number of Features:''' Total number of features (PEGs + RNAs)

'''Number of Warnings:''' Total number of non-fatal warning-conditions detected*.

'''Number of fatal problems:''' Total number of fatal error-conditions detected*.

<nowiki>*</nowiki>The difference between warnings and fatal problems is the impact on the RAST pipeline. While both are serious quality problems found by our automated control, only fatal problems require (your) intervention, eg. running the automated correction methods provided by the RAST pipeline. Please note that you can decide to apply all available automatic corrections during the upload.

Below you will find detailed explanations of these warnings and errors.

'''Possibly missing genes:'''
Crude but conservative estimate of the expected number of "undercalled" PEGs in the remaining gaps between features:

Estimated number of potentially "missing" PEGs :=
(number of base-pairs in gaps longer than 2 kbp) / (1 kbp/PEG)

Since the probability of a "random" gap longer than 2 kbp is less than 1 in 22000, such gaps are quite unlikely due to chance. Therefore the 2 kbp minimum gap threshold is very conservative, so the estimated number of "missing" PEGs should also be conservative.

== Gene problems ==

'''Genes with Bad Starts:'''
Non-truncated PEGs with non-ATG/GTG/TTG STARTs. These will be shown as warnings since we currently do not offer automated correction methods for them.

'''Genes with Bad Stops:'''
Non-truncated PEGs with non-TAA/TAG/TGA STOPs (Or whatever is appropriate for a variant genetic code). Bad STOPs should be considered fatal problems, but have been downgraded to "Warnings" as they should never occur in RAST.

'''Too Short''':
Number of PEGs shorter than the (default) threshold of 90 bp. Such PEGs are usually considered "lint".

== Overlaps ==

We recognize the following classes of overlaps:

'''Embedded PEGs:'''
Number of PEGs completely contained within another PEG. Considered a fatal error on first pass through the corrector. The following procedure is applied to automatically correct his error: If neither PEG is in a FIGfam, the embedded PEG is eliminated. If one PEG is in a FIGfam, automated removal eliminates the PEG that is not in a FIGfam. If both PEGs are in FIGfams, the shorter PEG is removed if it is less than half the length of the longer PEG. If an embedded PEG cannot be removed because both it and the PEG it is embedded in are in FIGfams and the PEGs have comparable lengths, then this problem is downgraded to a "Warning" so that processing may still proceed.

'''Bad RNA Overlaps:'''
Number of PEGs that overlap an RNA by more than the (default) threshold of 20 bp. Such overlaps are considered a fatal problem and the offending PEGs are unconditionally removed when automated correction has been selected.

'''Convergent overlaps:'''
Number of pairs of opposite-strand PEGs oriented towards each other, such that the STOP of each PEG is inside the other PEG, the START is not inside the other PEG, and the overlap exceeds the (default) threshold of 50 bp. Such overlaps are considered "Warning" conditions, not fatal.
Overlaps by less than threshold are not reported.

------->
<-------

'''Divergent overlaps:'''
Number of pairs of opposite-strand PEGs oriented away from each other, such that the START of each PEG is inside the other PEG, the STOP is not inside the other PEG, and the overlap exceeds the (default) threshold of 150 bp. Such overlaps are considered "Warning" conditions, not fatal.
Overlaps by less than threshold are not reported.

<-------
------->

'''Same-strand overlaps:'''
Number of pairs of same-strand PEGs oriented the same direction, such that overlap by more than the (default) threshold of 120 bp. Such overlaps are considered "Warning" conditions, not fatal.
(They are also a proxy for the number of frameshift errors.)

-------> <-------
-------> <-------

In addition there is flag that should never be reported to you. But just in case...

'''Impossible Overlap:'''
This serves as a code development flag. It is a "This Can't Happen!" condition that should never occur; if observed, it indicates that a severe logic error may exist within the overlap detection software.

MG RAST Tutorial

2007-12-18T03:02:57Z

Marland: /* MetaGenome Overview */

===Overview===

The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis.

Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes.

User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]].

The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago.

In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database].

===Registration===
Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required.

At the bottom of the main page is a like for registration (see Figure 1).

[[Image:mg-rast-main-page.jpeg]]

Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team.

Please note that your login and password are valid for use in both the MG-RAST and RAST servers.

===Submitting a Job===

Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job.

Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences.

Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help.

''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.''

An email will be sent once the automatic annotation has finished or in case user intervention is required.

===Viewing Results===
The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress.

The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs.

Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format.

===MetaGenome Overview===

The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found [[MG-RAST_Numbers|here]].

[[Image:MG-RAST-sample-overview.png]]

Users can search for a given function, subsystem or process in the table, or browse the Subsystem Overview. At the top right hand side of the page is a set of tabs that offer a wide set of information to browse, explore, compare and download. Browse allows users to look through the features of this metagenome either graphically or through a table. Both allow quick navigation and filtering for features of your interest. Each feature is linked to its own detail page. Explore allows users to view scenarios. Scenarios are isolated metabolic divisions that in aggregate represent the metabolic functionality of the metagenome. Each scenario is tested for reaction availability against the annotated functions. They provide the foundation for generating a metabolic reconstruction. Comparison of two metagenomes is also possible via the compare tab. You can also export all information about this metagenome (e.g. annotations, scenarios, subsystems) into a variety of formats (e.g. EMBL, Excel) for further analysis on your own system.

MG RAST Tutorial

2007-12-18T02:29:43Z

Marland: /* Registration */

File:MG-RAST-sample-overview.png

2007-12-18T02:29:03Z

Marland:

MG RAST Tutorial

2007-12-18T02:28:42Z

Marland: /* MetaGenome Overview */

===Overview===

The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis.

Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes.

User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]].

The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago.

In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database].

===Registration===
Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required.

At the bottom of the main page is a like for registration (see Figure 1).

[[image:mg-rast-main-page.jpeg]]

Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team.

Please note that your login and password are valid for use in both the MG-RAST and RAST servers.

===Submitting a Job===

Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job.

Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences.

Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help.

''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.''

An email will be sent once the automatic annotation has finished or in case user intervention is required.

===Viewing Results===
The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress.

The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs.

Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format.

===MetaGenome Overview===

The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found [[MG-RAST_Numbers|here]].

[[Image:MG-RAST-sample-overview.png]]

Users can search for a given function, subsystem or process in the table, or browse the Subsystem Overview.

File:mg-rast-sample-overview.png

2007-12-18T02:27:51Z

Marland:

MG RAST Tutorial

2007-12-18T02:26:25Z

Marland:

===Overview===

The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis.

Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes.

User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]].

The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago.

In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database].

===Registration===
Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required.

At the bottom of the main page is a like for registration (see Figure 1).

[[image:mg-rast-main-page.jpeg]]

Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team.

Please note that your login and password are valid for use in both the MG-RAST and RAST servers.

===Submitting a Job===

Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job.

Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences.

Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help.

''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.''

An email will be sent once the automatic annotation has finished or in case user intervention is required.

===Viewing Results===
The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress.

The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs.

Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format.

===MetaGenome Overview===

The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found [[MG-RAST_Numbers|here]].

[[Image:mg-rast-sample-overview.png]]

Users can search for a given function, subsystem or process in the table, or browse the Subsystem Overview.

MG RAST Tutorial

2007-12-18T02:25:45Z

Marland: /* MetaGenome Overview */

===Overview===

The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis.

Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes.

User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]].

The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago.

In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database].

===Registration===
Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required.

At the bottom of the main page is a like for registration (see Figure 1).

[[image:mg-rast-main-page.jpeg]]

Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team.

Please note that your login and password are valid for use in both the MG-RAST and RAST servers.

===Submitting a Job===

Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job.

Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences.

Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help.

''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.''

An email will be sent once the automatic annotation has finished or in case user intervention is required.

===Viewing Results===
The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress.

The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs.

Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format.

===MetaGenome Overview===

The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found [[MG-RAST_Numbers|here]].
[[Image:Mg-rast-sample-overview.png|300px]]

Users can search for a given function, subsystem or process in the table, or browse the Subsystem Overview.

MG RAST Tutorial

2007-12-18T02:24:55Z

Marland:

===Overview===

The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis.

Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes.

User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]].

The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago.

In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database].

===Registration===
Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required.

At the bottom of the main page is a like for registration (see Figure 1).

[[image:mg-rast-main-page.jpeg]]

Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team.

Please note that your login and password are valid for use in both the MG-RAST and RAST servers.

===Submitting a Job===

Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job.

Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences.

Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help.

''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.''

An email will be sent once the automatic annotation has finished or in case user intervention is required.

===Viewing Results===
The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress.

The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs.

Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format.

===MetaGenome Overview===

The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found [[MG-RAST_Numbers|here]].
[[Image:mg-rast-sample-overview.png|300px]]
[[Image:create_problem_set.png|300px]]

Users can search for a given function, subsystem or process in the table, or browse the Subsystem Overview.

MG RAST Tutorial

2007-12-18T02:23:36Z

Marland:

===Overview===

The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis.

Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes.

User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]].

The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago.

In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database].

===Registration===
Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required.

At the bottom of the main page is a like for registration (see Figure 1).

[[image:mg-rast-main-page.jpeg]]

Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team.

Please note that your login and password are valid for use in both the MG-RAST and RAST servers.

===Submitting a Job===

Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job.

Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences.

Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help.

''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.''

An email will be sent once the automatic annotation has finished or in case user intervention is required.

===Viewing Results===
The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress.

The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs.

Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format.

===MetaGenome Overview===

The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found [[MG-RAST_Numbers|here]].
[[image:mg-rast-sample-overview.PNG|300px]]

Users can search for a given function, subsystem or process in the table, or browse the Subsystem Overview.

MG RAST Tutorial

2007-12-18T02:22:03Z

Marland:

===Overview===

The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis.

Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes.

User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]].

The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago.

In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database].

===Registration===
Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required.

At the bottom of the main page is a like for registration (see Figure 1).

[[image:mg-rast-main-page.jpeg]]

Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team.

Please note that your login and password are valid for use in both the MG-RAST and RAST servers.

===Submitting a Job===

Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job.

Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences.

Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help.

''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.''

An email will be sent once the automatic annotation has finished or in case user intervention is required.

===Viewing Results===
The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress.

The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs.

Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format.

===MetaGenome Overview===

The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found [[MG-RAST_Numbers|here]].

[[image:mg-rast-sample-overview.PNG|300px]]

File:Mg-rast-sample-overview.PNG

2007-12-18T02:21:04Z

Marland:

MG RAST Tutorial

2007-12-18T02:20:35Z

Marland:

===Overview===

The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis.

Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes.

User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]].

The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago.

In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database].

===Registration===
Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required.

At the bottom of the main page is a like for registration (see Figure 1).

[[image:mg-rast-main-page.jpeg]]

Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team.

Please note that your login and password are valid for use in both the MG-RAST and RAST servers.

===Submitting a Job===

Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job.

Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences.

Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help.

''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.''

An email will be sent once the automatic annotation has finished or in case user intervention is required.

===Viewing Results===
The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress.

The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs.

Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format.

===MetaGenome Overview===
The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found [[MG-RAST_Numbers|here]].

[[image:mg-rast-sample-overview.PNG|300px]]

MG RAST Tutorial

2007-12-18T01:52:42Z

Marland:

===Overview===

The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis.

Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes.

User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly. In either case, the data needs to be in [[Valid fasta format]]. For more information, please see [[Which Sequences Should I Upload, and Where]]. For the metagenomics service please also read this explanation of [[metagenomics sequence formats]].

The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago.

In addition to SEED data we use the following ribosomal RNA databases for our analyses: [http://greengenes.lbl.gov/cgi-bin/nph-index.cgi greengenes], [http://rdp.cme.msu.edu/ RDP-II] and [http://bioinformatics.psb.ugent.be/webtools/rRNA/ European ribosomal RNA database].

===Registration===
Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required.

At the bottom of the main page is a like for registration (see Figure 1).

[[image:mg-rast-main-page.jpeg]]

Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team.

Please note that your login and password are valid for use in both the MG-RAST and RAST servers.

===Submitting a Job===

Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job.

Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences.

Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help.

''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.''

An email will be sent once the automatic annotation has finished or in case user intervention is required.

===Viewing Results===
The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress.

The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs.

Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found ("Browse annotated genome in SEED Viewer"). Users can also download the results in compressed GenBank format.

===MetaGenome Overview===
The MetaGenome Overview provides the user with various statistics regarding their metagenome and details on how each of these numbers are calculated can be found at MG-RAST_Numbers.

MG-RAST Numbers

2007-10-02T21:36:16Z

Marland:

The MG-RAST-Server and SEED Viewer offer you a large number of statistics and detailed numbers about your organism. The purpose of this page is to explain how we calculate these numbers and what they mean.

=== MG-RAST ===

On the details page of your organism, you will find the following numbers:

* ''Number of sequences''
: This is the total number of sequences submitted by the user for this genome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database.

* ''Total sequence length''
: This is the sum of the lengths (bp) of all submitted sequences.

* ''Average read length''
: This is the '''Total sequence length''' divided by the '''Number of sequences'''

* ''Longest sequence id'
: This is the identifier string of the longest sequence submitted.

* ''Longest sequence length''
: This is the length (bp) of the longest sequence submitted.

* ''Shortest sequence id''
: This is the identifier string of the shortest sequence submitted.

* ''Shortest sequence length''
: This is the length of the shortest sequence submitted

=== SeedViewer ===

On the ''Metagenome Overview'' page, there are a number of statistical counts about the selected metagenome:

* ''Size''
: This is the number of basepairs (total length) of all of the sequences submiited for a given metagenome.

: '''Known bug:''' Unfortunately there is currently a bug which shows a higher than actual sequence length. The MG-RAST Job Details page shows the correct sequence size.

* ''Number of Fragments''
: This is the number of submitted sequences which included at least one coding sequence that could be matched to our database.

* ''Number of Subsystems''
: The number of different subsystems where one or more functional roles were found in the submitted fragments of the metagenome.

* ''Number of Coding Sequences''
: The number of protein encoding genes found in the submitted fragments that matched against our database.
: '''Note:''' This number may be higher than the ''Number of Fragments'' if ...

* ''Number of RNAs''
: The number of RNAs found in the submitted fragments that matched against our database.

* ''Protein Encoding Genes''
: The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) and their sum should be the equal to the number of coding sequences displayed on the left.
: '''non-hypothetical'''
: This is the number of coding sequences, which were annotated with a function which is not hypothetical. Values for hypothetical include a list of synonyms like ''hypothetical protein'' or ''putative protein''
: '''hypothetical'''
: This is the number of coding sequences which were assigned to be hypothetical (or a synonym)

* ''Subsystem Counts''
The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role. Note that not every coding sequence is part of a subsystem and that a single CDS may be part of more than one subsytem.

=== SeedViewer - Taxonomy ===

The taxnomic classification is calculated in several independent ways. First, all sequences are compared to the different rDNA databases: (1) RDP, (2)the European Ribosomal Database project, and (3)Greengenes. The criteria for a sequence being similar is a BLASTN E value < 1x10-5 and at least 50nt in the alignment.

We also calculate the taxonomic profile of your sample from all the protein similarities computed to annotate the metagenome. The advantage of this approach is that we use a lot more data than is available for the 16S analysis, however, the disadvantage of this approach is that it is obviously limited to those genomes that are in our underlying SEED database.

RAST Tutorial

2007-08-24T18:15:45Z

Marland: Added toc

===The RAST Server Overview===

The RAST (Rapid Annotation using Subsystem Technology) Server provides high quality genome annotations for prokaryotes across the whole phylogenetic tree. It makes a SEED-quality annotation available as a service with a 48 hour turnaround time. The SEED environment and SEED data structures (most prominently FIGfams) are used to compute the automatic annotations; however data is not added into the SEED automatically. Once annotation is completed, genomes can be downloaded in a variety of formats or viewed online. The genome annotation provided does include a mapping of genes to subsystems and a metabolic reconstruction. Figure 1 provides an overview of the RAST Server and connections to the SEED Viewer.

Getting Started: Registration is required for genome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required.

[[Image:rast_fig1.jpg]]

Figure 1. Overview of the RAST Server navigation, features and capabilities.

===Jobs Overview===

Upon logging onto the server, users are directed to the “Jobs Overview” page, which as the name suggests, provides a site for job management. Jobs Overview has two main components: starting a new job and reviewing submitted/completed jobs.

Start a new job. The navigation bar (Figure 2) at the top of the page provides a pull down menu for job submission, logout, and review/edit user account information. To start a new job, users should select “Upload Genome” from the navigation bar or the link near the top of the page. The user is required to provide a valid taxonomy id+, the organism’s Genus, species, and strain, as well as a nucleotide sequence file in FASTA format. Optional parameters are suggested, but not required and include genetic code, sequencing method, coverage, number of contigs and average read length. Currently the server supports genome analysis of prokaryotes with genetic codes 4 and 11.

''+Taxonomy id’s can be obtained from the NCBI taxonomy browser (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/). Search by organism name, and the taxonomy id is returned. For example, Escherichia coli K12 has taxonomy id 83333.''

[[Image:rast_fig2.jpg]]

Figure 2. Jobs Overview Navigation Bar.

===Reviewing submitted/completed jobs===

The overall status of genome analysis can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Figure 3 shows an example account where the individual does not have any personal jobs, but has access to several for their organization. The table shows each job/genome and its status and contains information including job number, name of the user who started the job, genome id (taxonomy_id. internal_id), genome name, and annotation progress.

The table of jobs can be sorted on any column containing textual information. When the user has numerous genomes to select from, they can use the text boxes in the table header to search and refine the list of jobs.

Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the genome analysis can be found.

[[Image:rast_fig3.jpg]]

Figure 3. Jobs Overview for a given account.

===Job Details===

For a given job, the Job Details page provides the user with information regarding the status of the genome annotation progress, as well as access to the results of the analysis upon completion.

Account and job management links are found in the navigation bar at the top of the Job Details page (Figure 4) includes (1) logout, (2) upload a new genome, (3) link back to the Jobs Overview, and (4) review/edit your account information.

[[Image:rast_fig4.jpg]]

Figure 4. Job Details Navigation Bar.

The Job Details page has three main functions:

1. To provide access to the results of the genome analysis via the SEED Viewer,

2. Export tool that enables the user to download the annotated genome in various formats (GTF, GenBank, GFF3, or EMBL)

3. The status of their genome analysis. Information regarding the status of each major step in the analysis process is reported which includes:

* Genome upload
** Genome id and Name
** Job number
** Name of user who created the job
** Date and time of job submission
* Rapid propagation (protein function annotation)
* Quality check
** Statistics (number of features, warnings, fatal problems)
** Warnings (overlaps)
** Fatal Problems (embedded genes)
* Quality revision (users approval)
* Similarity Computation
* Bidirectional Best Hit Computation (for conserved regions and functional coupling)
* Auto Assignment (to subsystems)

File:Mg-rast-main-page.jpeg

2007-08-24T18:08:59Z

Marland:

MG RAST Tutorial

2007-08-24T18:08:28Z

Marland: Addition of first portion of MG-RAST tutorial.

===Overview===

The metagenomics RAST server (http://metagenomics.nmpdr.org) is a SEED-based environment that allows users to upload metagenomes for automated analyses. The server is built as a modified version of the RAST server. The RAST (Rapid Annotation using Subsystem Technology) technology was originally implemented to allow automated high-quality annotation of complete or draft microbial genomes using SEED data, and has been adapted for metagenome analysis.

Our freely available server provides the annotation of sequence fragments, their phylogenetic classification, functional classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic reconstruction for the metagenome and allows comparison of metabolic reconstructions of metagenomes and genomes.

User submission and analysis are confidential. Although we do not guarantee a maximum turnover time, the current average processing time is about 24 hours. Currently the server handles 454 and Sanger sequence data. Data sets supplied by 454 can be uploaded directly.

The server relies on the technology and data established by FIG and the NMPDR team at Argonne National Laboratory and the University of Chicago.

In addition to SEED data we use the following ribosomal RNA databases for our analyses: GREENGENES, RDP-II and European ribosomal RNA database.

===Registration===
Registration is required for metagenome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required.

At the bottom of the main page is a like for registration (see Figure 1).

[[image:mg-rast-main-page.jpeg]]

Required fields for registration include first and last name and your valid email address. Login information and other communication regarding the status of your metagenome analysis job(s) will be sent to the email address you provide. Optional information includes your organization and any notes you would like to send the rast server support team.

Please note that your login and password are valid for use in both the MG-RAST and RAST servers.

===Submitting a Job===

Once you have registered and logged into the server, you will be directed to your Jobs Overview. At the top of this page will be a link labeled "Upload Genome" which will allow you to start a new job.

Your metagenome file(s) should be uploaded as either a single plain text file containing all the sequences in FASTA format, or a gzip compressed tar archive (tar.gz) that has your FASTA sequences.

Please do not upload uncompressed files larger than 30 MB. If your data set is larger, use the compressed format or contact us for other options. If you would like, you can also include the quality files in your archive. The fasta file names should end either *.fna, *.fa, or *.fasta, and the quality files should be named *.qual. The quality files are not currently used in the analysis, but the sequences will be renamed and renumbered along with the fasta sequences. If you have trouble with the upload format please email mg-rast@mcs.anl.gov and we'll be happy to help.

''Data entered into the server will not be used for any purposes or integrated into the main SEED environment, it will remain on this server for 120 days or until deleted by the submitting user.''

An email will be sent once the automatic annotation has finished or in case user intervention is required.

===Viewing Results===
The overall status of your metagenome analyses can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Information includes each job/metagenome and its status and contains information including job number, name of the user who started the job, metagenome name, and annotation progress.

The table of jobs can be sorted on any column containing textual information. When the user has numerous metagenomes to select from, they can use the text boxes in the table header to search and refine the list of jobs.

Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the metagenome analysis can be found.

MediaWiki:Sidebar

2007-08-24T15:42:51Z

Marland: removal of bar

MediaWiki:Sidebar

2007-08-24T15:42:15Z

Marland: Addition of tutorial link for metagenomics RAST server.

* Navigation
** Home_of_the_SEED|Home of the SEED
** Annotating_1000_genomes|Manifesto
** SEED_People| SEED People
** Contact| Contact
* SEEDs
** http://seed-viewer.theseed.org/|SEED-Viewer
** http://theseed.uchicago.edu/FIG/index.cgi|Trial-SEED
* Applications
** http://rast.nmpdr.org/|RAST Annotation Server
** http://metagenomics.nmpdr.org/|Metagenomics RAST Server
* Documentation
** RAST_Tutorial|RAST Server Tutorial
** MG_RAST_Tutorial||MG-RAST Tutorial
** SEED_Viewer_Tutorial|SEED Viewer Tutorial
** Video_Tutorials|Video Tutorials
* Miscellaneous
** DownloadPage|Download Page
** Glossary|Glossary
** SOPs|SOPs
** SpecialPurposeDBs|Special Purpose DBs

Video Tutorials

2007-06-15T20:03:55Z

Marland:

'''RAST Sever Video Tutorials'''

* RAST User Registration ftp://ftp.theseed.org/misc/Workshop_AVIs/rast_registration.avi

* RAST Genome Submission ftp://ftp.theseed.org/misc/Workshop_AVIs/rast_upload.avi

* RAST Access and Export of Genome Analysis ftp://ftp.theseed.org/misc/Workshop_AVIs/rast_export.avi

Video Tutorials

2007-06-15T17:13:43Z

Marland:

'''RAST Sever Video Tutorials'''

* RAST User Registration :: [[Media:Example1.ogg]]

* RAST Genome Submission :: [[Media:Example2.ogg]]

* RAST Access and Export of Genome Analysis :: [[Media:Example3.ogg]]

MediaWiki:Sidebar

2007-06-15T17:06:03Z

Marland:

SEED Viewer Tutorial

2007-06-12T03:33:42Z

Marland:

'''The SEED Viewer'''

Selecting “Browse annotated genome in SEED Viewer” from the “Job Details” page of the RAST server will direct the user to the Organism Page in the SEED Viewer.

'''Organism Page in SEED Viewer'''

In the navigation bar at the top of the page adjacent to the homepage symbol is a pull down menu labeled 'This Organism' with the following 4 display options for this page:

[[Image:Seed_fig1.jpg]]

Figure 1. SEED Viewer navigation bar with links to the genome browser, genome features, reactions, and genome comparison tool.

1. Overview and Subsystems
* The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.
* A breakdown of the number of protein encoding genes with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.
* Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism.
* On the bottom left of the page a bar graph depicts the percentages of protein encoding genes for this genome that are present in at least one subsystem.
* Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems present in this genome by cellular process. At every level in the tree the number of protein encoding genes in each category is listed in parentheses. At the leaves of the tree are links to a Subsytem page in the SEED Viewer.

2. Browse Genome
* This display allows you to walk the chromosome of the selected genome.
* If the genome is not completely assembled, the first contig will be selected.
* The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu or the 'zoom in' or 'zoom out' buttons.
* The < and > buttons will move the window down or up the chromosome half the window size.
* The << and >> buttons will move the window down or up the chromosome a full window size.
* Under 'Options' you can select which features and the number of strands or reading frames displayed. By default the genome browser offers a two strand view of the currently selected organism.
* After selecting your options, click the 'Refresh' button to update the page.
* On the middle line of the chromosome display you will see features not associated with a reading frame, such as RNAs, pathogenicity islands or prophages.
* Hover over a feature in the chromosome display for a detailed description.
* Clicking an item will take you to the Annotation page in the SEED Viewer for this feature.

3. View Features
* Selecting this display provides a table containing feature ID, functional assignment, starting and stopping location in terms of base pairs relative to the beginning of the contig, feature type and a list of aliases.
* The total number of features for this genome is displayed above the table.
* Use the 'next>>' and 'last>>' links to quickly scroll through sets of 10 features.
* Filter features across the entire genome by using the text entry boxes in the 'Functional Assignment', 'Type' or 'Aliases' column header and then hitting enter.
* Sort or reverse sort the tables using the triangle in the columns headers.
* Export all or a subset of the features, after filtering, of a genome to a spreadsheet file using the 'Export Table' button.

4. View Reactions
* For each genome, the genes that are part of known subsystems are compiled as an expandable hierarchical tree. This organizes the subsystems present in this genome by cellular process.
* The next level in the tree shows all the reactions for a given cellular process with links to KEGG for complete reaction details.
* At the leaves of the tree are the fig ids for all proteins annotated as those which catalyze the reaction. These proteins are linked to an Annotation Overview in the SEED Viewer.

5. Compare Genome

This tool allows the user to identify protein functions that are the same or different for a set of organisms. The results are presented in tabular form with information regarding function, EC and subsystem involvement displayed. Each protein is linked to the Annotation Overview in the SEED Viewer.

6. Annotation Overview
* This page offers access to the data relating to a feature. By default the Overview version of the page is initially displayed providing the feature's function assignment, source organism, the role it performs in a subsystem, and a graphic displaying its genomic context. If this feature's function is associated with one or more functional roles, each functional role's name will be displayed and linked to a SEED Viewer Functional Role page. A part of a feature's function that is not also a functional role is NOT linked.
* If this feature is included in a subsystem, detailed information about this feature's role or roles in one or more subsystems is provided in a shaded box at the top of the page on the right. The functional role names and subsystem names are linked to the SEED Viewer Functional Role page and the SEED Viewer Subsystem page.
* In the graphic each line represents a different genome. The genome of the feature that is the subject of this page is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically distant to the subject feature's genome.
* If there are no close genomes only a single line for the subject feature's genome will be present.
* If no data for diverse genomes has been computed a message saying so will be be displayed.

''Sequence Data'' - From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the this feature's DNA sequence, DNA with flanking sequence or amino acid sequence.

''Tools'' - From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools to analyze this feature:
* TMpred (transmembrane helix prediction)
* TMHMM (transmembrane helix prediction)
* Gram negative PSORT (subcellular localization prediction)
* Gram negative SignalP (signal sequence prediction)
* Gram positive PSORT (subcellular localization prediction)
* Gram positive SignalP (signal sequence prediction)
* LipoP (lipoprotein prediction)
* InterProScan (protein domain identification)
* Radar (detection of protein sequence repeats)
* PPSearch (protein motif identification)
* Gram negative CELLO (subcellular localization prediction)
* Gram positive CELLO (subcellular localization prediction)
* ProDom (protein domain identification)

''Literature'' - This menu list links to sources of literature discussing this specific feature. Currently PubMed is the only source.

7. Functional Role
* This page displays statistics on the number of protein encoding genes within the SEED database that currently are associated with this functional role and within how many different organisms these genes are present.
* In addition, this page lists the subsystem(s) for a functional role and if present, EC number, associated GO terms, and KEGG reaction.
* A table lists all occurrences of the functional role in the SEED database.

[[Image:Seed_fig2.jpg]]

Figure 2. Flowchart for navigating the RAST Server and SEED Viewer. Arrows indicate how users can access the various pages within the system.

File:Seed fig2.jpg

2007-06-12T03:33:16Z

Marland:

File:Seed fig1.jpg

2007-06-12T03:32:57Z

Marland:

SEED Viewer Tutorial

2007-06-12T03:32:40Z

Marland:

'''The SEED Viewer'''

Selecting “Browse annotated genome in SEED Viewer” from the “Job Details” page of the RAST server will direct the user to the Organism Page in the SEED Viewer.

'''Organism Page in SEED Viewer'''

In the navigation bar at the top of the page adjacent to the homepage symbol is a pull down menu labeled 'This Organism' with the following 4 display options for this page:

[[Image:seed_fig1.jpg]]

Figure 1. SEED Viewer navigation bar with links to the genome browser, genome features, reactions, and genome comparison tool.

1. Overview and Subsystems
* The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.
* A breakdown of the number of protein encoding genes with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.
* Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism.
* On the bottom left of the page a bar graph depicts the percentages of protein encoding genes for this genome that are present in at least one subsystem.
* Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems present in this genome by cellular process. At every level in the tree the number of protein encoding genes in each category is listed in parentheses. At the leaves of the tree are links to a Subsytem page in the SEED Viewer.

2. Browse Genome
* This display allows you to walk the chromosome of the selected genome.
* If the genome is not completely assembled, the first contig will be selected.
* The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu or the 'zoom in' or 'zoom out' buttons.
* The < and > buttons will move the window down or up the chromosome half the window size.
* The << and >> buttons will move the window down or up the chromosome a full window size.
* Under 'Options' you can select which features and the number of strands or reading frames displayed. By default the genome browser offers a two strand view of the currently selected organism.
* After selecting your options, click the 'Refresh' button to update the page.
* On the middle line of the chromosome display you will see features not associated with a reading frame, such as RNAs, pathogenicity islands or prophages.
* Hover over a feature in the chromosome display for a detailed description.
* Clicking an item will take you to the Annotation page in the SEED Viewer for this feature.

3. View Features
* Selecting this display provides a table containing feature ID, functional assignment, starting and stopping location in terms of base pairs relative to the beginning of the contig, feature type and a list of aliases.
* The total number of features for this genome is displayed above the table.
* Use the 'next>>' and 'last>>' links to quickly scroll through sets of 10 features.
* Filter features across the entire genome by using the text entry boxes in the 'Functional Assignment', 'Type' or 'Aliases' column header and then hitting enter.
* Sort or reverse sort the tables using the triangle in the columns headers.
* Export all or a subset of the features, after filtering, of a genome to a spreadsheet file using the 'Export Table' button.

4. View Reactions
* For each genome, the genes that are part of known subsystems are compiled as an expandable hierarchical tree. This organizes the subsystems present in this genome by cellular process.
* The next level in the tree shows all the reactions for a given cellular process with links to KEGG for complete reaction details.
* At the leaves of the tree are the fig ids for all proteins annotated as those which catalyze the reaction. These proteins are linked to an Annotation Overview in the SEED Viewer.

5. Compare Genome

This tool allows the user to identify protein functions that are the same or different for a set of organisms. The results are presented in tabular form with information regarding function, EC and subsystem involvement displayed. Each protein is linked to the Annotation Overview in the SEED Viewer.

6. Annotation Overview
* This page offers access to the data relating to a feature. By default the Overview version of the page is initially displayed providing the feature's function assignment, source organism, the role it performs in a subsystem, and a graphic displaying its genomic context. If this feature's function is associated with one or more functional roles, each functional role's name will be displayed and linked to a SEED Viewer Functional Role page. A part of a feature's function that is not also a functional role is NOT linked.
* If this feature is included in a subsystem, detailed information about this feature's role or roles in one or more subsystems is provided in a shaded box at the top of the page on the right. The functional role names and subsystem names are linked to the SEED Viewer Functional Role page and the SEED Viewer Subsystem page.
* In the graphic each line represents a different genome. The genome of the feature that is the subject of this page is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically distant to the subject feature's genome.
* If there are no close genomes only a single line for the subject feature's genome will be present.
* If no data for diverse genomes has been computed a message saying so will be be displayed.

''Sequence Data'' - From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the this feature's DNA sequence, DNA with flanking sequence or amino acid sequence.

''Tools'' - From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools to analyze this feature:
* TMpred (transmembrane helix prediction)
* TMHMM (transmembrane helix prediction)
* Gram negative PSORT (subcellular localization prediction)
* Gram negative SignalP (signal sequence prediction)
* Gram positive PSORT (subcellular localization prediction)
* Gram positive SignalP (signal sequence prediction)
* LipoP (lipoprotein prediction)
* InterProScan (protein domain identification)
* Radar (detection of protein sequence repeats)
* PPSearch (protein motif identification)
* Gram negative CELLO (subcellular localization prediction)
* Gram positive CELLO (subcellular localization prediction)
* ProDom (protein domain identification)

''Literature'' - This menu list links to sources of literature discussing this specific feature. Currently PubMed is the only source.

7. Functional Role
* This page displays statistics on the number of protein encoding genes within the SEED database that currently are associated with this functional role and within how many different organisms these genes are present.
* In addition, this page lists the subsystem(s) for a functional role and if present, EC number, associated GO terms, and KEGG reaction.
* A table lists all occurrences of the functional role in the SEED database.

[[Image:seed_fig2.jpg]]

Figure 2. Flowchart for navigating the RAST Server and SEED Viewer. Arrows indicate how users can access the various pages within the system.

SEED Viewer Tutorial

2007-06-12T03:32:31Z

Marland:

'''The SEED Viewer'''

Selecting “Browse annotated genome in SEED Viewer” from the “Job Details” page of the RAST server will direct the user to the Organism Page in the SEED Viewer.

'''Organism Page in SEED Viewer'''

In the navigation bar at the top of the page adjacent to the homepage symbol is a pull down menu labeled 'This Organism' with the following 4 display options for this page:

[[Image:seed_fig1.jpg]]
Figure 1. SEED Viewer navigation bar with links to the genome browser, genome features, reactions, and genome comparison tool.

1. Overview and Subsystems
* The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.
* A breakdown of the number of protein encoding genes with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.
* Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism.
* On the bottom left of the page a bar graph depicts the percentages of protein encoding genes for this genome that are present in at least one subsystem.
* Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems present in this genome by cellular process. At every level in the tree the number of protein encoding genes in each category is listed in parentheses. At the leaves of the tree are links to a Subsytem page in the SEED Viewer.

2. Browse Genome
* This display allows you to walk the chromosome of the selected genome.
* If the genome is not completely assembled, the first contig will be selected.
* The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu or the 'zoom in' or 'zoom out' buttons.
* The < and > buttons will move the window down or up the chromosome half the window size.
* The << and >> buttons will move the window down or up the chromosome a full window size.
* Under 'Options' you can select which features and the number of strands or reading frames displayed. By default the genome browser offers a two strand view of the currently selected organism.
* After selecting your options, click the 'Refresh' button to update the page.
* On the middle line of the chromosome display you will see features not associated with a reading frame, such as RNAs, pathogenicity islands or prophages.
* Hover over a feature in the chromosome display for a detailed description.
* Clicking an item will take you to the Annotation page in the SEED Viewer for this feature.

3. View Features
* Selecting this display provides a table containing feature ID, functional assignment, starting and stopping location in terms of base pairs relative to the beginning of the contig, feature type and a list of aliases.
* The total number of features for this genome is displayed above the table.
* Use the 'next>>' and 'last>>' links to quickly scroll through sets of 10 features.
* Filter features across the entire genome by using the text entry boxes in the 'Functional Assignment', 'Type' or 'Aliases' column header and then hitting enter.
* Sort or reverse sort the tables using the triangle in the columns headers.
* Export all or a subset of the features, after filtering, of a genome to a spreadsheet file using the 'Export Table' button.

4. View Reactions
* For each genome, the genes that are part of known subsystems are compiled as an expandable hierarchical tree. This organizes the subsystems present in this genome by cellular process.
* The next level in the tree shows all the reactions for a given cellular process with links to KEGG for complete reaction details.
* At the leaves of the tree are the fig ids for all proteins annotated as those which catalyze the reaction. These proteins are linked to an Annotation Overview in the SEED Viewer.

5. Compare Genome

This tool allows the user to identify protein functions that are the same or different for a set of organisms. The results are presented in tabular form with information regarding function, EC and subsystem involvement displayed. Each protein is linked to the Annotation Overview in the SEED Viewer.

6. Annotation Overview
* This page offers access to the data relating to a feature. By default the Overview version of the page is initially displayed providing the feature's function assignment, source organism, the role it performs in a subsystem, and a graphic displaying its genomic context. If this feature's function is associated with one or more functional roles, each functional role's name will be displayed and linked to a SEED Viewer Functional Role page. A part of a feature's function that is not also a functional role is NOT linked.
* If this feature is included in a subsystem, detailed information about this feature's role or roles in one or more subsystems is provided in a shaded box at the top of the page on the right. The functional role names and subsystem names are linked to the SEED Viewer Functional Role page and the SEED Viewer Subsystem page.
* In the graphic each line represents a different genome. The genome of the feature that is the subject of this page is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically distant to the subject feature's genome.
* If there are no close genomes only a single line for the subject feature's genome will be present.
* If no data for diverse genomes has been computed a message saying so will be be displayed.

''Sequence Data'' - From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the this feature's DNA sequence, DNA with flanking sequence or amino acid sequence.

''Tools'' - From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools to analyze this feature:
* TMpred (transmembrane helix prediction)
* TMHMM (transmembrane helix prediction)
* Gram negative PSORT (subcellular localization prediction)
* Gram negative SignalP (signal sequence prediction)
* Gram positive PSORT (subcellular localization prediction)
* Gram positive SignalP (signal sequence prediction)
* LipoP (lipoprotein prediction)
* InterProScan (protein domain identification)
* Radar (detection of protein sequence repeats)
* PPSearch (protein motif identification)
* Gram negative CELLO (subcellular localization prediction)
* Gram positive CELLO (subcellular localization prediction)
* ProDom (protein domain identification)

''Literature'' - This menu list links to sources of literature discussing this specific feature. Currently PubMed is the only source.

7. Functional Role
* This page displays statistics on the number of protein encoding genes within the SEED database that currently are associated with this functional role and within how many different organisms these genes are present.
* In addition, this page lists the subsystem(s) for a functional role and if present, EC number, associated GO terms, and KEGG reaction.
* A table lists all occurrences of the functional role in the SEED database.

[[Image:seed_fig2.jpg]]

Figure 2. Flowchart for navigating the RAST Server and SEED Viewer. Arrows indicate how users can access the various pages within the system.

SEED Viewer Tutorial

2007-06-12T03:29:16Z

Marland:

'''The SEED Viewer'''

Selecting “Browse annotated genome in SEED Viewer” from the “Job Details” page of the RAST server will direct the user to the Organism Page in the SEED Viewer.

'''Organism Page in SEED Viewer'''

In the navigation bar at the top of the page adjacent to the homepage symbol is a pull down menu labeled 'This Organism' with the following 4 display options for this page:

Figure 5. SEED Viewer navigation bar with links to the genome browser, genome features, reactions, and genome comparison tool.

1. Overview and Subsystems
* The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.
* A breakdown of the number of protein encoding genes with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.
* Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism.
* On the bottom left of the page a bar graph depicts the percentages of protein encoding genes for this genome that are present in at least one subsystem.
* Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems present in this genome by cellular process. At every level in the tree the number of protein encoding genes in each category is listed in parentheses. At the leaves of the tree are links to a Subsytem page in the SEED Viewer.

2. Browse Genome
* This display allows you to walk the chromosome of the selected genome.
* If the genome is not completely assembled, the first contig will be selected.
* The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu or the 'zoom in' or 'zoom out' buttons.
* The < and > buttons will move the window down or up the chromosome half the window size.
* The << and >> buttons will move the window down or up the chromosome a full window size.
* Under 'Options' you can select which features and the number of strands or reading frames displayed. By default the genome browser offers a two strand view of the currently selected organism.
* After selecting your options, click the 'Refresh' button to update the page.
* On the middle line of the chromosome display you will see features not associated with a reading frame, such as RNAs, pathogenicity islands or prophages.
* Hover over a feature in the chromosome display for a detailed description.
* Clicking an item will take you to the Annotation page in the SEED Viewer for this feature.

3. View Features
* Selecting this display provides a table containing feature ID, functional assignment, starting and stopping location in terms of base pairs relative to the beginning of the contig, feature type and a list of aliases.
* The total number of features for this genome is displayed above the table.
* Use the 'next>>' and 'last>>' links to quickly scroll through sets of 10 features.
* Filter features across the entire genome by using the text entry boxes in the 'Functional Assignment', 'Type' or 'Aliases' column header and then hitting enter.
* Sort or reverse sort the tables using the triangle in the columns headers.
* Export all or a subset of the features, after filtering, of a genome to a spreadsheet file using the 'Export Table' button.

4. View Reactions
* For each genome, the genes that are part of known subsystems are compiled as an expandable hierarchical tree. This organizes the subsystems present in this genome by cellular process.
* The next level in the tree shows all the reactions for a given cellular process with links to KEGG for complete reaction details.
* At the leaves of the tree are the fig ids for all proteins annotated as those which catalyze the reaction. These proteins are linked to an Annotation Overview in the SEED Viewer.

5. Compare Genome
This tool allows the user to identify protein functions that are the same or different for a set of organisms. The results are presented in tabular form with information regarding function, EC and subsystem involvement displayed. Each protein is linked to the Annotation Overview in the SEED Viewer.

6. Annotation Overview
* This page offers access to the data relating to a feature. By default the Overview version of the page is initially displayed providing the feature's function assignment, source organism, the role it performs in a subsystem, and a graphic displaying its genomic context. If this feature's function is associated with one or more functional roles, each functional role's name will be displayed and linked to a SEED Viewer Functional Role page. A part of a feature's function that is not also a functional role is NOT linked.
* If this feature is included in a subsystem, detailed information about this feature's role or roles in one or more subsystems is provided in a shaded box at the top of the page on the right. The functional role names and subsystem names are linked to the SEED Viewer Functional Role page and the SEED Viewer Subsystem page.
* In the graphic each line represents a different genome. The genome of the feature that is the subject of this page is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically distant to the subject feature's genome.
* If there are no close genomes only a single line for the subject feature's genome will be present.
* If no data for diverse genomes has been computed a message saying so will be be displayed.

Sequence Data - From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the this feature's DNA sequence, DNA with flanking sequence or amino acid sequence.

Tools - From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools to analyze this feature:
* TMpred (transmembrane helix prediction)
* TMHMM (transmembrane helix prediction)
* Gram negative PSORT (subcellular localization prediction)
* Gram negative SignalP (signal sequence prediction)
* Gram positive PSORT (subcellular localization prediction)
* Gram positive SignalP (signal sequence prediction)
* LipoP (lipoprotein prediction)
* InterProScan (protein domain identification)
* Radar (detection of protein sequence repeats)
* PPSearch (protein motif identification)
* Gram negative CELLO (subcellular localization prediction)
* Gram positive CELLO (subcellular localization prediction)
* ProDom (protein domain identification)

Literature - This menu list links to sources of literature discussing this specific feature. Currently PubMed is the only source.

7. Functional Role
* This page displays statistics on the number of protein encoding genes within the SEED database that currently are associated with this functional role and within how many different organisms these genes are present.
* In addition, this page lists the subsystem(s) for a functional role and if present, EC number, associated GO terms, and KEGG reaction.
* A table lists all occurrences of the functional role in the SEED database.

Figure 6. Flowchart for navigating the RAST Server and SEED Viewer. Arrows indicate how users can access the various pages within the system.

File:rast fig3.jpg

2007-06-12T03:25:13Z

Marland:

RAST Tutorial

2007-06-12T03:24:42Z

Marland:

'''The RAST Server'''

The RAST (Rapid Annotation using Subsystem Technology) Server provides high quality genome annotations for prokaryotes across the whole phylogenetic tree. It makes a SEED-quality annotation available as a service with a 48 hour turnaround time. The SEED environment and SEED data structures (most prominently FIGfams) are used to compute the automatic annotations; however data is not added into the SEED automatically. Once annotation is completed, genomes can be downloaded in a variety of formats or viewed online. The genome annotation provided does include a mapping of genes to subsystems and a metabolic reconstruction. Figure 1 provides an overview of the RAST Server and connections to the SEED Viewer.

Getting Started: Registration is required for genome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required.

[[Image:rast_fig1.jpg]]

Figure 1. Overview of the RAST Server navigation, features and capabilities.

'''Jobs Overview'''

Upon logging onto the server, users are directed to the “Jobs Overview” page, which as the name suggests, provides a site for job management. Jobs Overview has two main components: starting a new job and reviewing submitted/completed jobs.

Start a new job. The navigation bar (Figure 2) at the top of the page provides a pull down menu for job submission, logout, and review/edit user account information. To start a new job, users should select “Upload Genome” from the navigation bar or the link near the top of the page. The user is required to provide a valid taxonomy id+, the organism’s Genus, species, and strain, as well as a nucleotide sequence file in FASTA format. Optional parameters are suggested, but not required and include genetic code, sequencing method, coverage, number of contigs and average read length. Currently the server supports genome analysis of prokaryotes with genetic codes 4 and 11.

''+Taxonomy id’s can be obtained from the NCBI taxonomy browser (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/). Search by organism name, and the taxonomy id is returned. For example, Escherichia coli K12 has taxonomy id 83333.''

[[Image:rast_fig2.jpg]]

Figure 2. Jobs Overview Navigation Bar.

'''Reviewing submitted/completed jobs.'''

The overall status of genome analysis can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Figure 3 shows an example account where the individual does not have any personal jobs, but has access to several for their organization. The table shows each job/genome and its status and contains information including job number, name of the user who started the job, genome id (taxonomy_id. internal_id), genome name, and annotation progress.

The table of jobs can be sorted on any column containing textual information. When the user has numerous genomes to select from, they can use the text boxes in the table header to search and refine the list of jobs.

Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the genome analysis can be found.

[[Image:rast_fig3.jpg]]

Figure 3. Jobs Overview for a given account.

''' Job Details'''

For a given job, the Job Details page provides the user with information regarding the status of the genome annotation progress, as well as access to the results of the analysis upon completion.

Account and job management links are found in the navigation bar at the top of the Job Details page (Figure 4) includes (1) logout, (2) upload a new genome, (3) link back to the Jobs Overview, and (4) review/edit your account information.

[[Image:rast_fig4.jpg]]

Figure 4. Job Details Navigation Bar.

The Job Details page has three main functions:

1. To provide access to the results of the genome analysis via the SEED Viewer,

2. Export tool that enables the user to download the annotated genome in various formats (GTF, GenBank, GFF3, or EMBL)

3. The status of their genome analysis. Information regarding the status of each major step in the analysis process is reported which includes:

* Genome upload
** Genome id and Name
** Job number
** Name of user who created the job
** Date and time of job submission
* Rapid propagation (protein function annotation)
* Quality check
** Statistics (number of features, warnings, fatal problems)
** Warnings (overlaps)
** Fatal Problems (embedded genes)
* Quality revision (users approval)
* Similarity Computation
* Bidirectional Best Hit Computation (for conserved regions and functional coupling)
* Auto Assignment (to subsystems)

File:Rast fig4.jpg

2007-06-12T03:23:38Z

Marland:

File:Rast fig3.jpg

2007-06-12T03:23:14Z

Marland:

RAST Tutorial

2007-06-12T03:22:59Z

Marland:

RAST Tutorial

2007-06-12T03:22:02Z

Marland:

'''The RAST Server'''

The RAST (Rapid Annotation using Subsystem Technology) Server provides high quality genome annotations for prokaryotes across the whole phylogenetic tree. It makes a SEED-quality annotation available as a service with a 48 hour turnaround time. The SEED environment and SEED data structures (most prominently FIGfams) are used to compute the automatic annotations; however data is not added into the SEED automatically. Once annotation is completed, genomes can be downloaded in a variety of formats or viewed online. The genome annotation provided does include a mapping of genes to subsystems and a metabolic reconstruction. Figure 1 provides an overview of the RAST Server and connections to the SEED Viewer.

Getting Started: Registration is required for genome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required.

[[Image:rast_fig1.jpg]]

Figure 1. Overview of the RAST Server navigation, features and capabilities.

'''Jobs Overview'''

Upon logging onto the server, users are directed to the “Jobs Overview” page, which as the name suggests, provides a site for job management. Jobs Overview has two main components: starting a new job and reviewing submitted/completed jobs.

Start a new job. The navigation bar (Figure 2) at the top of the page provides a pull down menu for job submission, logout, and review/edit user account information. To start a new job, users should select “Upload Genome” from the navigation bar or the link near the top of the page. The user is required to provide a valid taxonomy id+, the organism’s Genus, species, and strain, as well as a nucleotide sequence file in FASTA format. Optional parameters are suggested, but not required and include genetic code, sequencing method, coverage, number of contigs and average read length. Currently the server supports genome analysis of prokaryotes with genetic codes 4 and 11.

''+Taxonomy id’s can be obtained from the NCBI taxonomy browser (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/). Search by organism name, and the taxonomy id is returned. For example, Escherichia coli K12 has taxonomy id 83333.''

[[Image:rast_fig2.jpg]]

Figure 2. Jobs Overview Navigation Bar.

'''Reviewing submitted/completed jobs.'''

The overall status of genome analysis can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Figure 3 shows an example account where the individual does not have any personal jobs, but has access to several for their organization. The table shows each job/genome and its status and contains information including job number, name of the user who started the job, genome id (taxonomy_id. internal_id), genome name, and annotation progress.

The table of jobs can be sorted on any column containing textual information. When the user has numerous genomes to select from, they can use the text boxes in the table header to search and refine the list of jobs.

Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the genome analysis can be found.

Figure 3. Jobs Overview for a given account.

''' Job Details'''

For a given job, the Job Details page provides the user with information regarding the status of the genome annotation progress, as well as access to the results of the analysis upon completion.

Account and job management links are found in the navigation bar at the top of the Job Details page (Figure 4) includes (1) logout, (2) upload a new genome, (3) link back to the Jobs Overview, and (4) review/edit your account information.

Figure 4. Job Details Navigation Bar.

The Job Details page has three main functions:

1. To provide access to the results of the genome analysis via the SEED Viewer,

2. Export tool that enables the user to download the annotated genome in various formats (GTF, GenBank, GFF3, or EMBL)

3. The status of their genome analysis. Information regarding the status of each major step in the analysis process is reported which includes:

* Genome upload
** Genome id and Name
** Job number
** Name of user who created the job
** Date and time of job submission
* Rapid propagation (protein function annotation)
* Quality check
** Statistics (number of features, warnings, fatal problems)
** Warnings (overlaps)
** Fatal Problems (embedded genes)
* Quality revision (users approval)
* Similarity Computation
* Bidirectional Best Hit Computation (for conserved regions and functional coupling)
* Auto Assignment (to subsystems)

RAST Tutorial

2007-06-12T03:15:50Z

Marland:

'''The RAST Server'''

The RAST (Rapid Annotation using Subsystem Technology) Server provides high quality genome annotations for prokaryotes across the whole phylogenetic tree. It makes a SEED-quality annotation available as a service with a 48 hour turnaround time. The SEED environment and SEED data structures (most prominently FIGfams) are used to compute the automatic annotations; however data is not added into the SEED automatically. Once annotation is completed, genomes can be downloaded in a variety of formats or viewed online. The genome annotation provided does include a mapping of genes to subsystems and a metabolic reconstruction. Figure 1 provides an overview of the RAST Server and connections to the SEED Viewer.

Getting Started: Registration is required for genome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required.

[[Image:rast_fig1.jpg]]

Figure 1. Overview of the RAST Server navigation, features and capabilities.

'''Jobs Overview'''

Upon logging onto the server, users are directed to the “Jobs Overview” page, which as the name suggests, provides a site for job management. Jobs Overview has two main components: starting a new job and reviewing submitted/completed jobs.

Start a new job. The navigation bar (Figure 2) at the top of the page provides a pull down menu for job submission, logout, and review/edit user account information. To start a new job, users should select “Upload Genome” from the navigation bar or the link near the top of the page. The user is required to provide a valid taxonomy id+, the organism’s Genus, species, and strain, as well as a nucleotide sequence file in FASTA format. Optional parameters are suggested, but not required and include genetic code, sequencing method, coverage, number of contigs and average read length. Currently the server supports genome analysis of prokaryotes with genetic codes 4 and 11.

''+Taxonomy id’s can be obtained from the NCBI taxonomy browser (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/). Search by organism name, and the taxonomy id is returned. For example, Escherichia coli K12 has taxonomy id 83333.''

[[Image:rast_fig2.jpg]]
Figure 2. Jobs Overview Navigation Bar.

'''Reviewing submitted/completed jobs.'''

The overall status of genome analysis can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Figure 3 shows an example account where the individual does not have any personal jobs, but has access to several for their organization. The table shows each job/genome and its status and contains information including job number, name of the user who started the job, genome id (taxonomy_id. internal_id), genome name, and annotation progress.

The table of jobs can be sorted on any column containing textual information. When the user has numerous genomes to select from, they can use the text boxes in the table header to search and refine the list of jobs.

Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the genome analysis can be found.

Figure 3. Jobs Overview for a given account.

''' Job Details'''

For a given job, the Job Details page provides the user with information regarding the status of the genome annotation progress, as well as access to the results of the analysis upon completion.

Account and job management links are found in the navigation bar at the top of the Job Details page (Figure 4) includes (1) logout, (2) upload a new genome, (3) link back to the Jobs Overview, and (4) review/edit your account information.

Figure 4. Job Details Navigation Bar.

The Job Details page has three main functions:
1. To provide access to the results of the genome analysis via the SEED Viewer,
2. Export tool that enables the user to download the annotated genome in various formats (GTF, GenBank, GFF3, or EMBL)
3. The status of their genome analysis. Information regarding the status of each major step in the analysis process is reported which includes:
o Genome upload
o Genome id and Name
o Job number
o Name of user who created the job
o Date and time of job submission
o Rapid propagation (protein function annotation)
o Quality check
o Statistics (number of features, warnings, fatal problems)
o Warnings (overlaps)
o Fatal Problems (embedded genes)
o Quality revision (users approval)
o Similarity Computation
o Bidirectional Best Hit Computation (for conserved regions and functional coupling)
o Auto Assignment (to subsystems)

File:Rast fig2.jpg

2007-06-12T03:14:48Z

Marland:

RAST Tutorial

2007-06-12T03:12:29Z

Marland:

'''The RAST Server'''

The RAST (Rapid Annotation using Subsystem Technology) Server provides high quality genome annotations for prokaryotes across the whole phylogenetic tree. It makes a SEED-quality annotation available as a service with a 48 hour turnaround time. The SEED environment and SEED data structures (most prominently FIGfams) are used to compute the automatic annotations; however data is not added into the SEED automatically. Once annotation is completed, genomes can be downloaded in a variety of formats or viewed online. The genome annotation provided does include a mapping of genes to subsystems and a metabolic reconstruction. Figure 1 provides an overview of the RAST Server and connections to the SEED Viewer.

Getting Started: Registration is required for genome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required.

[[Image:rast_fig1.jpg]]

Figure 1. Overview of the RAST Server navigation, features and capabilities.

'''Jobs Overview'''

Upon logging onto the server, users are directed to the “Jobs Overview” page, which as the name suggests, provides a site for job management. Jobs Overview has two main components: starting a new job and reviewing submitted/completed jobs.

Start a new job. The navigation bar (Figure 2) at the top of the page provides a pull down menu for job submission, logout, and review/edit user account information. To start a new job, users should select “Upload Genome” from the navigation bar or the link near the top of the page. The user is required to provide a valid taxonomy id+, the organism’s Genus, species, and strain, as well as a nucleotide sequence file in FASTA format. Optional parameters are suggested, but not required and include genetic code, sequencing method, coverage, number of contigs and average read length. Currently the server supports genome analysis of prokaryotes with genetic codes 4 and 11.

''+Taxonomy id’s can be obtained from the NCBI taxonomy browser (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/). Search by organism name, and the taxonomy id is returned. For example, Escherichia coli K12 has taxonomy id 83333.''

Figure 2. Jobs Overview Navigation Bar.

'''Reviewing submitted/completed jobs.'''

The overall status of genome analysis can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Figure 3 shows an example account where the individual does not have any personal jobs, but has access to several for their organization. The table shows each job/genome and its status and contains information including job number, name of the user who started the job, genome id (taxonomy_id. internal_id), genome name, and annotation progress.

The table of jobs can be sorted on any column containing textual information. When the user has numerous genomes to select from, they can use the text boxes in the table header to search and refine the list of jobs.

Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the genome analysis can be found.

Figure 3. Jobs Overview for a given account.

''' Job Details'''

For a given job, the Job Details page provides the user with information regarding the status of the genome annotation progress, as well as access to the results of the analysis upon completion.

Account and job management links are found in the navigation bar at the top of the Job Details page (Figure 4) includes (1) logout, (2) upload a new genome, (3) link back to the Jobs Overview, and (4) review/edit your account information.

Figure 4. Job Details Navigation Bar.

The Job Details page has three main functions:
1. To provide access to the results of the genome analysis via the SEED Viewer,
2. Export tool that enables the user to download the annotated genome in various formats (GTF, GenBank, GFF3, or EMBL)
3. The status of their genome analysis. Information regarding the status of each major step in the analysis process is reported which includes:
o Genome upload
o Genome id and Name
o Job number
o Name of user who created the job
o Date and time of job submission
o Rapid propagation (protein function annotation)
o Quality check
o Statistics (number of features, warnings, fatal problems)
o Warnings (overlaps)
o Fatal Problems (embedded genes)
o Quality revision (users approval)
o Similarity Computation
o Bidirectional Best Hit Computation (for conserved regions and functional coupling)
o Auto Assignment (to subsystems)

RAST Tutorial

2007-06-11T21:39:47Z

Marland:

'''The RAST Server'''

The RAST (Rapid Annotation using Subsystem Technology) Server provides high quality genome annotations for prokaryotes across the whole phylogenetic tree. It makes a SEED-quality annotation available as a service with a 48 hour turnaround time. The SEED environment and SEED data structures (most prominently FIGfams) are used to compute the automatic annotations; however data is not added into the SEED automatically. Once annotation is completed, genomes can be downloaded in a variety of formats or viewed online. The genome annotation provided does include a mapping of genes to subsystems and a metabolic reconstruction. Figure 1 provides an overview of the RAST Server and connections to the SEED Viewer.

Getting Started: Registration is required for genome submission and viewing of results. This enables us to contact users once the computation is finished and in case the users intervention is required.

[[Image:Rast_fig1.jpg]]

Figure 1. Overview of the RAST Server navigation, features and capabilities.

'''Jobs Overview'''

Upon logging onto the server, users are directed to the “Jobs Overview” page, which as the name suggests, provides a site for job management. Jobs Overview has two main components: starting a new job and reviewing submitted/completed jobs.

Start a new job. The navigation bar (Figure 2) at the top of the page provides a pull down menu for job submission, logout, and review/edit user account information. To start a new job, users should select “Upload Genome” from the navigation bar or the link near the top of the page. The user is required to provide a valid taxonomy id+, the organism’s Genus, species, and strain, as well as a nucleotide sequence file in FASTA format. Optional parameters are suggested, but not required and include genetic code, sequencing method, coverage, number of contigs and average read length. Currently the server supports genome analysis of prokaryotes with genetic codes 4 and 11.

''+Taxonomy id’s can be obtained from the NCBI taxonomy browser (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/). Search by organism name, and the taxonomy id is returned. For example, Escherichia coli K12 has taxonomy id 83333.''

Figure 2. Jobs Overview Navigation Bar.

'''Reviewing submitted/completed jobs.'''

The overall status of genome analysis can be viewed from the main portion of the Jobs Overview page. This contains information regarding a user’s personal jobs and when applicable, jobs of the user’s organization. Figure 3 shows an example account where the individual does not have any personal jobs, but has access to several for their organization. The table shows each job/genome and its status and contains information including job number, name of the user who started the job, genome id (taxonomy_id. internal_id), genome name, and annotation progress.

The table of jobs can be sorted on any column containing textual information. When the user has numerous genomes to select from, they can use the text boxes in the table header to search and refine the list of jobs.

Clicking on the bars for a given job in the annotation progress column directs the user to the “Job Details” page where the detailed job status and access to the genome analysis can be found.

Figure 3. Jobs Overview for a given account.

''' Job Details'''

For a given job, the Job Details page provides the user with information regarding the status of the genome annotation progress, as well as access to the results of the analysis upon completion.

Account and job management links are found in the navigation bar at the top of the Job Details page (Figure 4) includes (1) logout, (2) upload a new genome, (3) link back to the Jobs Overview, and (4) review/edit your account information.

Figure 4. Job Details Navigation Bar.

The Job Details page has three main functions:
1. To provide access to the results of the genome analysis via the SEED Viewer,
2. Export tool that enables the user to download the annotated genome in various formats (GTF, GenBank, GFF3, or EMBL)
3. The status of their genome analysis. Information regarding the status of each major step in the analysis process is reported which includes:
o Genome upload
o Genome id and Name
o Job number
o Name of user who created the job
o Date and time of job submission
o Rapid propagation (protein function annotation)
o Quality check
o Statistics (number of features, warnings, fatal problems)
o Warnings (overlaps)
o Fatal Problems (embedded genes)
o Quality revision (users approval)
o Similarity Computation
o Bidirectional Best Hit Computation (for conserved regions and functional coupling)
o Auto Assignment (to subsystems)

File:rast fig2.jpg

2007-06-11T21:36:18Z

Marland:

File:rast fig1.jpg

2007-06-11T21:21:28Z

Marland:

File:Rast fig1.jpg

2007-06-11T21:19:21Z

Marland: Overview of the RAST server and its connections to the SEED viewer.

Overview of the RAST server and its connections to the SEED viewer.