The SEED: an Annotation/Analysis Tool Provided by FIG
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SEED version cvs.1257362800 (Wed Nov 4 13:26:40 2009) on anno-3.nmpdr.org		 The SEED

FIG search

Welcome to TheSEED.uchicago.edu. This is running from a June 15, 2009, snapshot of the master data. If you need access to the previous version of this SEED, it is available at http://theseed.uchicago.edu/prev/FIG/index.cgi.

Contains 64 archaeal, 990 bacterial, 562 eukaryal, 1341 viral and 2 environmental genomes

Of these, 47 archaeal, 736 bacterial and 29 eukaryal genomes are more-or-less complete

Work on Subsystems

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Or, on this machine you can: Use the new Subsystem Editor

Work on FIGfams

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Searching for Genes or Functional Roles Using Text

UniProt WebService Search
Search Pattern: Search
User ID: [optional]     Max Genes:     Max Roles:

If You Need to Pick a Genome for Options Below

 [Log]

812 genomes shown
Show some of the selected genome 		Domain(s) to show:



   

Completeness?

Finding Candidates for a Functional Role

Make sure that you type the functional role you want to search for in the Search Pattern above

Metabolic Overviews and Subsystem Maps (via KEGG & SEED) - Choose Map



Searching DNA or Protein Sequences (in a selected organism)

Sequence/Pattern:
Search Program: Program Options:

Exporting Assignments

Extract assignments made by (do not prefix with master:)
Save as user: (do not prefix with master:)
After date (MM/DD/YYYY)





Alternatively, you can generate a set of assignments as translations of existing assignments. To do so, you need to make sure that you fill in the Save as user field just above. You should use something like RossO (leave out the master:). When you look at the assignments (and decide which to actually install), they will be made available under that name (but, when you access them, you will normally be using something like master:RossO)

From:

To:    
Help with generate assignments via translation

Searching for Interesting Genes

Process Saved Assignments Sets

Here you should include the master:. Thus use something like master:RossO

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Locate clustered genes not in subsystems


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Align Sequences

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Locate PEGs in Subsystems

If you wish to locate PEGs in subsystems, you have two approaches supported. You can give a FIG id, and you will get a list of all homologs in the designated genome that occur in subsystems. Alternatively, you can specify a functional role, and all PEGs in the genome that match that role will be shown.
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Genome:
Search:
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Compare Metabolic Reconstructions

If you wish to compare the reconstructions for two distinct genomes, use this tool. You should specify two genomes, or a P1K server output directory (as genome1) and a second genome (which must be a valid genome ID that exists in this SEED). You can ask for functional roles/subsystems that the genomes have in common, those that exist in genome1 only, or those that exist in only genome2.
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Genome1:

Genome2:
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Compare Genomes

If you wish to compare the contents of several genomes, you can use this tool. Choose a set of genomes (at least two).

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Optionally, you can select a PEG and window size to limit the comparison:
PEG:
Window Size:

New Pattern Matching

The new pattern location tool.

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Pattern: