TheSeed - User contributions [en]

MediaWiki:Sidebar

2010-08-18T19:24:46Z

BruceParrello:

* 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|Public-SEED
** http://pseed.theseed.org/|PATRIC SEED
* Applications
** http://blog.theseed.org/servers/|Servers Blog
** http://blog.theseed.org/model_seed/|Model SEED Blog
** http://rast.nmpdr.org/|RAST Annotation Server
** http://metagenomics.nmpdr.org/|Metagenomics RAST Server
** http://blog.theseed.org/servers/2010/07/scan-for-matches.html| Scan for Matches (patscan)
* Documentation
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial
** SEED_Viewer_Tutorial|SEED Viewer Tutorial
* Miscellaneous
** DownloadPage|Download Page
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions
** Glossary|Glossary
** SOPs|SOPs
** SpecialPurposeDBs|Special Purpose DBs

MediaWiki:Sidebar

2010-08-18T19:23:03Z

BruceParrello:

* 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|Public-SEED
** http://pseed.theseed.org/|PATRIC SEED
* Applications
** http://blog.theseed.org/servers/|Servers Blog
** http://blog.theseed.org/model_seed/|Model SEED Blog
** http://rast.nmpdr.org/|RAST Annotation Server
** http://metagenomics.nmpdr.org/|Metagenomics RAST Server
** http://blog.theseed.org/servers/2010/07/scan-for-matches.html Scan for Matches (patscan)
* Documentation
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial
** SEED_Viewer_Tutorial|SEED Viewer Tutorial
* Miscellaneous
** DownloadPage|Download Page
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions
** Glossary|Glossary
** SOPs|SOPs
** SpecialPurposeDBs|Special Purpose DBs

MediaWiki:Sidebar

2010-08-12T20:32:29Z

BruceParrello:

* 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|Public-SEED
** http://pseed.theseed.org/|PATRIC SEED
* Applications
** http://blog.theseed.org/servers/|Servers Blog
** http://blog.theseed.org/model_seed/|Model SEED Blog
** http://rast.nmpdr.org/|RAST Annotation Server
** http://metagenomics.nmpdr.org/|Metagenomics RAST Server
* Documentation
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial
** SEED_Viewer_Tutorial|SEED Viewer Tutorial
* Miscellaneous
** DownloadPage|Download Page
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions
** Glossary|Glossary
** SOPs|SOPs
** SpecialPurposeDBs|Special Purpose DBs

MediaWiki:Sidebar

2010-08-12T19:49:49Z

BruceParrello:

* 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|Public-SEED
** http://pseed.theseed.org/|PATRIC SEED
* Applications
** http://blog.theseed.org/servers/|Servers Blog
** http://rast.nmpdr.org/|RAST Annotation Server
** http://metagenomics.nmpdr.org/|Metagenomics RAST Server
* Documentation
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial
** SEED_Viewer_Tutorial|SEED Viewer Tutorial
* Miscellaneous
** DownloadPage|Download Page
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions
** Glossary|Glossary
** SOPs|SOPs
** SpecialPurposeDBs|Special Purpose DBs

MediaWiki:Sidebar

2010-08-10T19:14:43Z

BruceParrello:

* 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|Public-SEED
** http://pseed.theseed.org/|PATRIC SEED
* Applications
** http://blog.theseed.org/servers/|Network-Based SEED API
** http://rast.nmpdr.org/|RAST Annotation Server
** http://metagenomics.nmpdr.org/|Metagenomics RAST Server
* Documentation
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial
** SEED_Viewer_Tutorial|SEED Viewer Tutorial
* Miscellaneous
** DownloadPage|Download Page
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions
** Glossary|Glossary
** SOPs|SOPs
** SpecialPurposeDBs|Special Purpose DBs

MediaWiki:Sidebar

2010-08-10T19:11:39Z

BruceParrello:

* 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|Public-SEED
** http://pseed.theseed.org/|PATRIC SEED
* Applications
** http://servers.nmpdr.org/|Network-Based SEED API
** http://blog.theseed.org/servers/|Servers Blog
** http://rast.nmpdr.org/|RAST Annotation Server
** http://metagenomics.nmpdr.org/|Metagenomics RAST Server
* Documentation
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial
** SEED_Viewer_Tutorial|SEED Viewer Tutorial
* Miscellaneous
** DownloadPage|Download Page
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions
** Glossary|Glossary
** SOPs|SOPs
** SpecialPurposeDBs|Special Purpose DBs

MediaWiki:Sidebar

2009-12-16T18:08:11Z

BruceParrello:

* 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|Public-SEED
* Applications
** http://servers.nmpdr.org/|Network-Based SEED API
** http://rast.nmpdr.org/|RAST Annotation Server
** http://metagenomics.nmpdr.org/|Metagenomics RAST Server
* Documentation
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial
** SEED_Viewer_Tutorial|SEED Viewer Tutorial
* Miscellaneous
** DownloadPage|Download Page
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions
** Glossary|Glossary
** SOPs|SOPs
** SpecialPurposeDBs|Special Purpose DBs

MediaWiki:Sidebar

2009-12-16T18:07:34Z

BruceParrello:

* 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|Public-SEED
* Applications
** http://servers.nmpdr.org/|SEED Servers
** http://rast.nmpdr.org/|RAST Annotation Server
** http://metagenomics.nmpdr.org/|Metagenomics RAST Server
* Documentation
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST|RAST Server Tutorial
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/MG-RAST|MG-RAST Tutorial
** SEED_Viewer_Tutorial|SEED Viewer Tutorial
* Miscellaneous
** DownloadPage|Download Page
** http://www.nmpdr.org/FIG/wiki/view.cgi/Main/FAQS|FAQ Frequently Asked Questions
** Glossary|Glossary
** SOPs|SOPs
** SpecialPurposeDBs|Special Purpose DBs

Species group

2007-07-31T22:56:01Z

BruceParrello: First version

A species group is a group of related organisms in the NMPDR. There are specific groups for the NMPDR [[core organisms]]. The remaining organisms are in a single group. Sometimes this latter group is referred to as the ''supporting group''. In the [[Genome Control]], the supporting organisms are split by domain. In the [[NMPDR Search Results]], the core organisms are shown first and the supporting group is shown below that.

Genome Control

2007-07-31T22:45:37Z

BruceParrello: First real version

The Genome Control is a powerful tool for selecting one or more genomes. It lists every genome available in the NMPDR, sorted by [[species group]] and color-coded by domain. Bacteria are shaded light pink, archaea are light blue, and eukaryota are yellow. The species groups for the NMPDR [[core organisms]] are placed at the top, and the other genes are shown at the bottom, separated by domain.

[[Image:GenomeControl.png]]

The genome list is a classic HTML list control. Clicking a genome selects it and deselects all others. Use CTRL-click to toggle individual genomes and SHIFT-click to select a range of genomes.

Below the genome list is a text box and a long button labeled '''Select genomes containing'''. This is called the ''Instant Search Bar''. Put any string in the text box, click the '''Select genomes containing''' button, and each genome with the specified string in its name will be selected. The string you type can be a genus name, a species name, a unique characterization, or a taxonomy number. In the box above, the two genomes shown were selected by typing '''vulnificus'''. Typing '''Vibrio''' would select all Vibrio genomes. Typing '''83333''' would select ''E Coli K12''. Genome selection by this method is always additive: in other words, if you typed '''strep''' into the text box in the situation shown above, as it is shown above the ''Vibrio vulnificus'' genomes would remain selected. To start from scratch with a blank list, click the '''Clear All''' button.

Below the Instant Search Bar are three special-purpose buttons.

* '''Clear All''' deselects all the genomes.
* '''Select All''' selects all the genomes.
* '''Select NMPDR''' selects all NMPDR [[core organisms]] and deselects the others.

At the bottom of the control is a list of the genomes you've selected. The list box only shows a small number of genomes at a time, but the Selected-Genomes display will always include the complete list of genomes selected.

Genome Control

2007-07-31T21:39:14Z

BruceParrello: Safety save

File:GenomeControl.png

2007-07-30T23:14:17Z

BruceParrello: NMPDR Genome selection control

NMPDR Genome selection control

Keyword Box

2007-07-29T19:17:10Z

BruceParrello: Added notes on using negation

The NMPDR keyword search works like a typical search engine. You type in the appropriate words, and a list of genes will come back. Our keyword database contains millions of words, including ''vitamins'', ''aldolase'', and ''pyrophosphokinase''. The NMPDR looks at nine specific data items when computing the keywords for a gene. The table below shows each of the nine steps along with the keywords derived by that step for the gene '''fig|171101.1.peg.269''', a dual-role protein encoding gene for ''Streptococcus pneumoniae r6'' that has 40 keywords.

{|border="2"
| '''FIG gene identifier''' || fig|171101.1.peg.269
|-
| '''The [[Alias|aliases]]''' || GeneID:934668, gi|15902313, kegg|spd:SPD_0272, kegg|spr:spr0269, NP_357863.1, sp|P59657, spr0269, sulD, tr|Q04MF8, uni|P59657, uni|Q04MF8
|-
| '''All words in the functional role''' || Dihydroneopterin, aldolase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase amino, hydroxy, hydroxymethyldihydropteridine
|-
| '''The genome ID''' || 171101.1
|-
| '''All words in the taxonomy''' || bacteria, firmicutes, lactobacillales, streptococcaceae, streptococcus, pneumoniae, r6
|-
| '''The [[subsystem]] names and classifications''' || folate, biosynthesis, cofactors, vitamins, prosthetic, groups, pigments, folates, pterines
|-
| '''The EC number''' || 2.7.6.3, 4.1.2.25
|-
| '''The [[subsystem role]] || 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine
|-
| '''Special Keywords''' || essential
|}

====Notes====

* Some keywords appear twice.
* In the functional role, hyphenated words are stored in their full form (''2-amino-4-hydroxy-6-hydroxymethyldihydropteridine'') as well as broken up on the hyphen boundaries ('''amino hydroxy hydroxymethyldihydropteridine''').
* Keywords are case-insensitive.
* Special keywords indicate attributes of the gene. Most of these are incomplete: for example, we know certain genes are virulence-associated, but for most of the genes we have no virulence data.
** ''virulence'', which indicates the gene participates in the process of helping the organism to damage its host. This attribute is incomplete.
** ''essential'', which indicates that the gene is essential to to the survival of the organism. This attribute is incomplete.
** ''iedb'', which indicates that the gene is listed in the [http://www.immuneepitope.org/home.do Immune Epitope Database]

===Advanced Keyword Searching===

Normally, the search process selects the genes relevant to all the words in the keyword box. You can modify the default behavior using the following control characters.

{|border="2"
| '''char''' || '''Meaning''' || '''Example''' || '''Explanation of Example'''
|-
| '''-''' || negation || 2.7.6.3 '''-'''firmicutes || search for all genes with EC number 2.7.6.3 that are not in firmicutes
|-
| '''()''' || optional || '''('''2.7.6.3 4.1.2.25''')''' || search for any gene with EC number 2.7.6.3 or 4.1.2.25
|-
| '''""''' || phrase || '''"'''folate biosynthesis'''"''' || search for all genes that participate in folate biosynthesis
|}

===Using Negation===

It is illegal to use negation on all the keywords. For example, you can't do

-hypothetical

to get all non-hypothetical proteins. You can trick the the keyword search a little by including a positive keyword for a broad category

bacteria -hypothetical

which will return all non-hypothetical proteins for bacteria. This is not recommended, however, because you will get over a million results.

Queries that rely primarily on negation make the most sense when your result set is already restricted.

Keyword Box

2007-07-28T20:51:53Z

BruceParrello: First real version

The NMPDR keyword search works like a typical search engine. You type in the appropriate words, and a list of genes will come back. Our keyword database contains millions of words, including ''vitamins'', ''aldolase'', and ''pyrophosphokinase''. The NMPDR looks at nine specific data items when computing the keywords for a gene. The table below shows each of the nine steps along with the keywords derived by that step for the gene '''fig|171101.1.peg.269''', a dual-role protein encoding gene for ''Streptococcus pneumoniae r6'' that has 40 keywords.

{|border="2"
| '''FIG gene identifier''' || fig|171101.1.peg.269
|-
| '''The [[Alias|aliases]]''' || GeneID:934668, gi|15902313, kegg|spd:SPD_0272, kegg|spr:spr0269, NP_357863.1, sp|P59657, spr0269, sulD, tr|Q04MF8, uni|P59657, uni|Q04MF8
|-
| '''All words in the functional role''' || Dihydroneopterin, aldolase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase amino, hydroxy, hydroxymethyldihydropteridine
|-
| '''The genome ID''' || 171101.1
|-
| '''All words in the taxonomy''' || bacteria, firmicutes, lactobacillales, streptococcaceae, streptococcus, pneumoniae, r6
|-
| '''The [[subsystem]] names and classifications''' || folate, biosynthesis, cofactors, vitamins, prosthetic, groups, pigments, folates, pterines
|-
| '''The EC number''' || 2.7.6.3, 4.1.2.25
|-
| '''The [[subsystem role]] || 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine
|-
| '''Special Keywords''' || essential
|}

====Notes====

* Some keywords appear twice.
* In the functional role, hyphenated words are stored in their full form (''2-amino-4-hydroxy-6-hydroxymethyldihydropteridine'') as well as broken up on the hyphen boundaries ('''amino hydroxy hydroxymethyldihydropteridine''').
* Keywords are case-insensitive
* Special keywords indicate attributes of the gene. Most of these are incomplete: for example, we know certain genes are virulence-associated, but for most of the genes we have no virulence data.
** ''virulence'', which indicates the gene participates in the process of helping the organism to damage its host. This attribute is incomplete.
** ''essential'', which indicates that the gene is essential to to the survival of the organism. This attribute is incomplete.
** ''iedb'', which indicates that the gene is listed in the [http://www.immuneepitope.org/home.do Immune Epitope Database]

===Advanced Keyword Searching===

Normally, the search process selects the genes relevant to all the words in the keyword box. You can modify the default behavior using the following control characters.

{|border="2"
| '''char''' || '''Meaning''' || '''Example''' || '''Explanation of Example'''
|-
| '''-''' || negation || 2.7.6.3 '''-'''firmicutes || search for all genes with EC number 2.7.6.3 that are not in firmicutes
|-
| '''()''' || optional || '''('''2.7.6.3 4.1.2.25''')''' || search for any gene with EC number 2.7.6.3 or 4.1.2.25
|-
| '''""''' || phrase || '''"'''folate biosynthesis'''"''' || search for all genes that participate in folate biosynthesis
|}

Keyword Box

2007-07-28T20:05:44Z

BruceParrello: safety save

The NMPDR keyword search works like a typical search engine. You type in the appropriate words, and a list of genes will come back. Our keyword database contains millions of words, including ''vitamins'', ''aldolase'', and ''pyrophosphokinase''. The NMPDR looks at nine specific data items when computing the keywords for a gene. The table below shows each of the nine steps along with the keywords derived by that step for the gene '''fig|171101.1.peg.269''', a dual-role protein encoding gene for ''Streptococcus pneumoniae r6'' that has 40 keywords.

{|
| '''FIG gene identifier''' || fig|171101.1.peg.269
|-
| '''The [[Alias|aliases]]''' || GeneID:934668, gi|15902313, kegg|spd:SPD_0272, kegg|spr:spr0269, NP_357863.1, sp|P59657, spr0269, sulD, tr|Q04MF8, uni|P59657, uni|Q04MF8
|-
| '''All words in the functional role''' || Dihydroneopterin, aldolase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase amino, hydroxy, hydroxymethyldihydropteridine
|-
| '''The genome ID''' || 171101.1
|-
| '''All words in the taxonomy''' || bacteria, firmicutes, lactobacillales, streptococcaceae, streptococcus, pneumoniae, r6
|-
| '''The [[subsystem]] names and classifications''' || folate, biosynthesis, cofactors, vitamins, prosthetic, groups, pigments, folates, pterines
|-
| '''The EC number''' || 2.7.6.3, 4.1.2.25
|-
| '''The [[subsystem role]] || 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine
|-
| '''Special Keywords''' || essential
|}

====Notes====

* Some keywords appear twice.
* In the functional role, hyphenated words are stored in their full form (''2-amino-4-hydroxy-6-hydroxymethyldihydropteridine'') as well as broken up on the hyphen boundaries ('''amino- hydroxy hydroxymethyldihydropteridine''').
* Keywords are case-insensitive
* Special keywords indicate attributes of the gene. Most of these are incomplete: for example, we know certain genes are virulence-associated, but for most of the genes we have no virulence data.
** ''virulence'', which indicates the gene participates in the process of helping the organism to damage its host. This attribute is incomplete.
** ''essential'', which indicates that the gene is essential to to the survival of the organism. This attribute is incomplete.
** ''iedb'', which indicates that the gene is listed in the [http://www.immuneepitope.org/home.do Immune Epitope Database]

===Advanced Keyword Searching===

Normally, the search process selects the genes relevant to all the words in the keyword box. You can modify the default behavior by prefixing control characters to the keywords.

{|
|Char|Meaning|Example|Explanation of Example
|-
|'''-'''|negation|'''2.7.6.3 -firmicutes''': search for all genes with EC number 2.7.6.3 that are not in firmicutes
|-
|'''()'''|optional|

Keyword Box

2007-07-28T19:10:43Z

BruceParrello: Changed to a more complicated example gene

The NMPDR keyword search works like a typical search engine. You type in the appropriate words, and a list of genes will come back.

The keywords for a specified gene are as follows. The examples shown are for the gene '''fig|171101.1.peg.269''', which is sulD for ''Streptococcus pneumoniae R6''.

{|
| '''FIG gene identifier''' || fig|171101.1.peg.269
|-
| '''The [[Alias|aliases]]''' || GeneID:934668, gi|15902313, kegg|spd:SPD_0272, kegg|spr:spr0269, NP_357863.1, sp|P59657, spr0269, sulD, tr|Q04MF8, uni|P59657, uni|Q04MF8
|-
| '''All words in the functional role''' || Dihydroneopterin, aldolase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase amino, hydroxy, hydroxymethyldihydropteridine
|-
| '''The genome ID''' || 171101.1
|-
| '''All words in the taxonomy''' || bacteria, firmicutes, lactobacillales, streptococcaceae, streptococcus, pneumoniae, r6
|-
| '''The [[subsystem]] names and classifications''' || folate, biosynthesis, cofactors, vitamins, prosthetic, groups, pigments, folates, pterines
|-
| '''The EC number''' || 2.7.6.3, 4.1.2.25
|-
| '''The [[subsystem role]] || 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine
|-
| '''Special Keywords''' || essential
|}

Notes

* In the functional role, hyphenated words are stored in their full form (''2-amino-4-hydroxy-6-hydroxymethyldihydropteridine'') as well as broken up on the hyphen boundaries ('''amino- hydroxy hydroxymethyldihydropteridine''').
* Keywords are case-insensitive
* Special keywords indicate attributes of the gene. The list of special keywords currently supported appears below.
** ''virulence'', which indicates the gene participates in the process of helping the organism to damage its host
** ''essential'', which indicates that the gene is essential to to the survival of the organism
** ''iedb'', which indicates that the gene is listed in the [http://www.immuneepitope.org/home.do Immune Epitope Database]

Keyword Box

2007-07-28T18:33:07Z

BruceParrello: safety save

The NMPDR keyword search works like a typical search engine. You type in the appropriate words, and a list of genes will come back.

The keywords for a specified gene are as follows. The examples shown are for the gene '''fig|100226.1.peg.3361''', which is EC 2.7.6.3 for ''Streptomyces coelicolor A3(2)''.

{|
| '''FIG gene identifier''' || fig|100226.1.peg.3361
|-
| '''The [[Alias|aliases]]''' || GeneID:1098838, gi|21221828, kegg|sco:SCO3401, NP_627607.1, SCO3401, tr|Q9X8I1, uni|Q9X8I1
|-
| '''All words in the functional role''' || 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine
|-
| '''The genome ID''' || 100226.1
|-
| '''All words in the taxonomy''' || bacteria, actinobacteria, actinobacteridae, actinomycetales, streptomycineae, streptomycetaceae, streptomyces, coelicolor, a32
|-
| '''The [[subsystem]] names and classifications''' || folate, biosynthesis, cofactors, vitamins, prosthetic, groups, pigments, folates, pterines
|-
| '''The EC number''' || 2.7.6.3
|-
| '''The [[subsystem role]] || 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine, pyrophosphokinase, amino, hydroxy, hydroxymethylhydroperidine
|-
| '''Special Keywords''' ||
|}

Notes

* In the functional role, hyphenated words are stored in their full form (''2-amino-4-hydroxy-6-hydroxymethyldihydropteridine'') as well as broken up on the hyphen boundaries ('''amino- hydroxy hydroxymethyldihydropteridine''').
* The subsystem role for this gene is the same as the functional role.
* Keywords are case-insensitive
* Special keywords

Keyword Box

2007-07-28T18:19:49Z

BruceParrello: safety save

Alias

2007-07-28T17:33:27Z

BruceParrello: First real version

An alias is a gene identifier from an outside organization or database. Inside the NMPDR's data structures, the [[FIG ID]] is used for each gene. Each gene also has a list of aliases. There may be none, or there may be a dozen.

Refseq IDs are included without change, but most of the other aliases use a prefix to identify the type. The prefix ends with either a vertical bar (|) or colon (:). For example, the gene with a FIG ID of fig|100226.1.peg.3361 has the following aliases.

* '''GeneID:1098838''', its Gene ID
* '''gi|21221828''', its [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=21221828&dopt=GenPept Genbank ID]
* '''kegg|sco:SCO3401''', its [http://www.genome.ad.jp/dbget-bin/www_bget?sco+SCO3401 KEGG ID]
* '''NP_627607.1''', its [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein;cmd=search;term=NP_627607.1 Refseq ID]
* '''LocusTag:SCO3401''', its locus tag
* '''tr|Q9X8I1''', its [http://ca.expasy.org/uniprot/Q9X8I1 TREMBL ID]
* '''uni|Q9X8I1''', its [http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinAc=Q9X8I1 UniProt ID]

Gene names (e.g. '''dnaK''' or '''grpE''') are also considered aliases.

Alias

2007-07-28T17:23:05Z

BruceParrello: Safety save

DrugSearch

2007-07-28T10:02:46Z

BruceParrello:

One of the projects underway at the NMPDR is generating ''in silico'' docking results for proteins that are believed to be good drug targets. For each selected protein, its PDB is selected from the [http://www.rcsb.org/pdb/ Protein Data Bank] and compared against a database of over 3 million ligands taken from the [http://blaster.docking.org/zinc/ ZINC database]. For each PDB put through this process, the NMPDR selects from 55 to 60 significant results. The results are displayed on the Drug Target Search Form. Simply select a PDB in the dropdown box, and the docking energies computed for the ligands will be displayed.

The energies displayed are in kcal/mol. The total energy is divided into two components: '''Van der Waals''' energy is computed from the shapes of the interlocking surfaces; '''Electrostatic''' energy is computed from the electrical attraction between the molecules.

DrugSearch

2007-07-26T19:48:55Z

BruceParrello:

One of the projects underway at the NMPDR is generating ''in silico'' docking results for proteins that are believed to be good drug targets. For each selected protein, its PDB is selected from the [http://www.rcsb.org/pdb/ Protein Data Bank] and compared against a database of over 3 million ligands taken from the [http://blaster.docking.org/zinc/ ZINC database]. For each PDB put through this process, the NMPDR selects from 55 to 60 significant results. The results are displayed on the Drug Target Search Form. Simply select a PDB in the dropdown box, and the docking energies computed for the ligands will be displayed.

The energies displayed are in kcal/mol. The total energy is divided into two components: '''Van der Waals''' energy is computed by the shapes of the interlocking surfaces; '''Electrostatic''' energy is computed from the electrical attraction between the molecules.

NMPDR Search

2007-07-26T17:51:49Z

BruceParrello: Sorted the list of search types into alphabetical order

The NMPDR search facility provides many different ways to look for genes, genomes, or sequences in the NMPDR database. The following searches are currently supported.

{|
| '''[[DrugSearch]]''' || Show ''in silico'' docking results for select PDBs.
|-
| '''[[FidSearch]]''' || Display genes from one or more genomes filtered by subsystem or keywords.
|-
| '''[[OpSearch]]''' || Display genes of a single genome organized into operons.
|-
| '''[[SigGenes]]''' || Display genes that are common to a set of genomes, or that differentiate between two sets of genomes.
|-
| '''[[SubSearch]]''' || Search for genes in a given subsystem or subsystem class.
|-
| '''[[ToolSearch]]''' || Search for genes or DNA using BLAST or pattern-matching.
|-
| '''[[WordSearch]]''' || Display genes that match certain keywords.
|}

The results of a search will generally start with data for the NMPDR [[core organisms]]. All NMPDR searches allow you to download results in tab-delimited and XML formats. NMPDR searches that return a list of genes also allow you to download the genes in FASTA format.

Most NMPDR searches use a powerful [[Genome Control]] that allows you to choose one or more genomes according to various criteria. Some also use a search-engine style [[Keyword Box]]. The Keyword Box can also be found at the top of many of the NMPDR pages.

If you have a question about something in an NMPDR search form, mouse over the a question mark to get a hint. Click on the blue question mark to pop up the Wiki page on the subject. The blue question marks have been circled in the sample search form below.

[[Image:BlueQuestionMarks.png]]

Core organisms

2007-07-26T17:49:33Z

BruceParrello:

NMPDR is a [http://www.brc-central.org/cgi-bin/prok_manatee/brc-central/brc_central.cgi Bioinformatics Resource Center]. Each center specializes in certain pathogens. In NMPDR, we call these the ''core genomes'' or ''NMPDR genomes''. The genomes not in the core set are considered ''supporting genomes''.

On the [[Genome Control]] and in [[NMPDR Search Results]], the core genomes are shown first.

The NMPDR core genomes come from the following generae or species:

* [http://www.nmpdr.org/content/campy.php Campylobacter]
* [http://www.nmpdr.org/content/listeria.php Listeria]
* [http://www.nmpdr.org/content/staph.php Staphylococcus aureus]
* [http://www.nmpdr.org/content/strep.php Streptococcus]
* [http://www.nmpdr.org/content/vibrio.php Vibrio]

For some genera, such as Vibrio, the genomes are divided into subgroups by species, or by pathogenicity. These subgroups are displayed in the Genome Control.

Although the core genomes are our primary focus, any complete genome for which we have reliable annotations is copied to the NMPDR as a supporting genome; however, not all of the search attributes are computed for all of the supporting genomes. Check the individual search pages (accessible from [[NMPDR Search]]) for more information about this.

NMPDR Search

2007-07-26T16:53:06Z

BruceParrello:

The NMPDR search facility provides many different ways to look for genes, genomes, or sequences in the NMPDR database. The following searches are currently supported.

{|
| '''[[OpSearch]]''' || Display genes of a single genome organized into operons.
|-
| '''[[WordSearch]]''' || Display genes that match certain keywords.
|-
| '''[[FidSearch]]''' || Display genes from one or more genomes filtered by subsystem or keywords.
|-
| '''[[SigGenes]]''' || Display genes that are common to a set of genomes, or that differentiate between two sets of genomes.
|-
| '''[[ToolSearch]]''' || Search for genes or DNA using BLAST or pattern-matching.
|-
| '''[[SubSearch]]''' || Search for genes in a given subsystem or subsystem class.
|-
| '''[[DrugSearch]]''' || Show ''in silico'' docking results for select PDBs.
|}

The results of a search will generally start with data for the NMPDR [[core organisms]]. All NMPDR searches allow you to download results in tab-delimited and XML formats. NMPDR searches that return a list of genes also allow you to download the genes in FASTA format.

Most NMPDR searches use a powerful [[Genome Control]] that allows you to choose one or more genomes according to various criteria. Some also use a search-engine style [[Keyword Box]]. The Keyword Box can also be found at the top of many of the NMPDR pages.

If you have a question about something in an NMPDR search form, mouse over the a question mark to get a hint. Click on the blue question mark to pop up the Wiki page on the subject. The blue question marks have been circled in the sample search form below.

[[Image:BlueQuestionMarks.png]]

File:BlueQuestionMarks.png

2007-07-26T16:50:07Z

BruceParrello: Highlights the blue question marks in a search form. This is a second attempt to upload this picture; I am conducting experiments to see if I can get the picture to work consistently.

Highlights the blue question marks in a search form. This is a second attempt to upload this picture; I am conducting experiments to see if I can get the picture to work consistently.

NMPDR Search

2007-07-25T21:25:53Z

BruceParrello: Trying to fix the stupid image

The NMPDR search facility provides many different ways to look for genes, genomes, or sequences in the NMPDR database. The following searches are currently supported.

{|
| '''[[OpSearch]]''' || Display genes of a single genome organized into operons.
|-
| '''[[WordSearch]]''' || Display genes that match certain keywords.
|-
| '''[[FidSearch]]''' || Display genes from one or more genomes filtered by subsystem or keywords.
|-
| '''[[SigGenes]]''' || Display genes that are common to a set of genomes, or that differentiate between two sets of genomes.
|-
| '''[[ToolSearch]]''' || Search for genes or DNA using BLAST or pattern-matching.
|-
| '''[[SubSearch]]''' || Search for genes in a given subsystem or subsystem class.
|-
| '''[[DrugSearch]]''' || Show ''in silico'' docking results for select PDBs.
|}

The results of a search will generally start with data for the NMPDR [[core organisms]]. All NMPDR searches allow you to download results in tab-delimited and XML formats. NMPDR searches that return a list of genes also allow you to download the genes in FASTA format.

Most NMPDR searches use a powerful [[Genome Control]] that allows you to choose one or more genomes according to various criteria. Some also use a search-engine style [[Keyword Box]]. The Keyword Box can also be found at the top of many of the NMPDR pages.

If you have a question about something in an NMPDR search form, mouse over the a question mark to get a hint. Click on the blue question mark to pop up the Wiki page on the subject. The blue question marks have been circled in the sample search form below.

[[Image:BlueQMarks.png]]

NMPDR Search

2007-07-23T21:35:01Z

BruceParrello:

The NMPDR search facility provides many different ways to look for genes, genomes, or sequences in the NMPDR database. The following searches are currently supported.

{|
| '''[[OpSearch]]''' || Display genes of a single genome organized into operons.
|-
| '''[[WordSearch]]''' || Display genes that match certain keywords.
|-
| '''[[FidSearch]]''' || Display genes from one or more genomes filtered by subsystem or keywords.
|-
| '''[[SigGenes]]''' || Display genes that are common to a set of genomes, or that differentiate between two sets of genomes.
|-
| '''[[ToolSearch]]''' || Search for genes or DNA using BLAST or pattern-matching.
|-
| '''[[SubSearch]]''' || Search for genes in a given subsystem or subsystem class.
|-
| '''[[DrugSearch]]''' || Show ''in silico'' docking results for select PDBs.
|}

The results of a search will generally start with data for the NMPDR [[core organisms]]. All NMPDR searches allow you to download results in tab-delimited and XML formats. NMPDR searches that return a list of genes also allow you to download the genes in FASTA format.

Most NMPDR searches use a powerful [[Genome Control]] that allows you to choose one or more genomes according to various criteria. Some also use a search-engine style [[Keyword Box]]. The Keyword Box can also be found at the top of many of the NMPDR pages.

If you have a question about something in an NMPDR search form, mouse over the a question mark to get a hint. Click on the blue question mark to pop up the Wiki page on the subject. The blue question marks have been circled in the sample search form below.

[[Image:BlueQMarks.png|Sample search form]]

NMPDR Search

2007-07-23T21:31:34Z

BruceParrello: Added image and text about the hint buttons

The NMPDR search facility provides many different ways to look for genes, genomes, or sequences in the NMPDR database. The following searches are currently supported.

{|
| '''[[OpSearch]]''' || Display genes of a single genome organized into operons.
|-
| '''[[WordSearch]]''' || Display genes that match certain keywords.
|-
| '''[[FidSearch]]''' || Display genes from one or more genomes filtered by subsystem or keywords.
|-
| '''[[SigGenes]]''' || Display genes that are common to a set of genomes, or that differentiate between two sets of genomes.
|-
| '''[[ToolSearch]]''' || Search for genes or DNA using BLAST or pattern-matching.
|-
| '''[[SubSearch]]''' || Search for genes in a given subsystem or subsystem class.
|-
| '''[[DrugSearch]]''' || Show ''in silico'' docking results for select PDBs.
|}

The results of a search will generally start with data for the NMPDR [[core organisms]]. All NMPDR searches allow you to download results in tab-delimited and XML formats. NMPDR searches that return a list of genes also allow you to download the genes in FASTA format.

Most NMPDR searches use a powerful [[Genome Control]] that allows you to choose one or more genomes according to various criteria. Some also use a search-engine style [[Keyword Box]]. The Keyword Box can also be found at the top of many of the NMPDR pages.

If you have a question about something in an NMPDR search form, mouse over the blue question mark to get a hint. Click on the blue question mark to pop up the Wiki page on the subject. The blue question marks have been circled in the sample search form below.

[[Image:BlueQMarks.png|Sample search form]]

File:BlueQMarks.png

2007-07-23T21:23:19Z

BruceParrello: A sample NMPDR search form with the blue question marks highlighted.

A sample NMPDR search form with the blue question marks highlighted.

NMPDR Search

2007-07-23T20:48:47Z

BruceParrello: An overview of the NMPDR search facility

The NMPDR search facility provides many different ways to look for genes, genomes, or sequences in the NMPDR database. The following searches are currently supported.

{|
| '''[[OpSearch]]''' || Display genes of a single genome organized into operons.
|-
| '''[[WordSearch]]''' || Display genes that match certain keywords.
|-
| '''[[FidSearch]]''' || Display genes from one or more genomes filtered by subsystem or keywords.
|-
| '''[[SigGenes]]''' || Display genes that are common to a set of genomes, or that differentiate between two sets of genomes.
|-
| '''[[ToolSearch]]''' || Search for genes or DNA using BLAST or pattern-matching.
|-
| '''[[SubSearch]]''' || Search for genes in a given subsystem or subsystem class.
|-
| '''[[DrugSearch]]''' || Show ''in silico'' docking results for select PDBs.
|}

The results of a search will generally start with data for the NMPDR [[core organisms]]. All NMPDR searches allow you to download results in tab-delimited and XML formats. NMPDR searches that return a list of genes also allow you to download the genes in FASTA format.

Most NMPDR searches use a powerful [[Genome Control]] that allows you to choose one or more genomes according to various criteria. Some also use a search-engine style [[Keyword Box]]. The Keyword Box can also be found at the top of many of the NMPDR pages.

NMPDR Search

2007-07-23T20:48:25Z

BruceParrello: An overview of the NMPDR search facility

The NMPDR search facility provides many different ways to look for genes, genomes, or sequences in the NMPDR database. The following searches are currently supported.

{|
| '''[[OpSearch]]''' || Display genes of a single genome organized into operons.
|-
| '''[[WordSearch]]''' || Display genes that match certain keywords.
|-
| '''[[FidSearch]]''' || Display genes from one or more genomes filtered by subsystem or keywords.
|-
| '''[[SigGenes]]''' || Display genes that are common to a set of genomes, or that differentiate between two sets of genomes.
|-
| '''[[ToolSearch]]''' || Search for genes or DNA using BLAST or pattern-matching.
|-
| '''[[SubSearch]]''' || Search for genes in a given subsystem or subsystem class.
|-
| '''[[DrugSearch]]''' || Show ''in silico'' docking results for select PDBs.
|}

The results of a search will generally start with data for the NMPDR [[core organisms]]. All NMPDR searches allow you to download results in tab-delimited and XML formats. NMPDR searches that return a list of genes also allow you to download the genes in FASTA format.

Most NMPDR searches use a powerful [[Genome Control]] that allows you to choose one or more genomes according to various criteria. Some also use a search-engine style [[Keyword Box]]. The Keyword Box can also be found at the top of many of the NMPDR pages.

NMPDR Search

2007-07-23T20:43:05Z

BruceParrello: Overview of the NMPDR Search Facility