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Re: [HCLSIG] homologs for yeast proteins?

From: Alf Eaton <lists@hubmed.org>
Date: Tue, 31 Jan 2006 15:56:30 -0500
Message-ID: <43DFCEFE.4070902@hubmed.org>
To: public-semweb-lifesci@w3.org

Eric Jain wrote:
> 
> Joanne Luciano wrote:
>> An MD I met with last week mentioned briefly the desire to obtain 
>> homologs
>> for yeast proteins with the GO ID 0031930.  With it was a request for 
>> other
>> suggestions for querying proteins with this ontology assignment 
>> (looking for
>> mammalian homologs).
>>
>> Can the semantic web help with this or is it already basic and solved, in
>> which case, can someone point me or fill in the details?  Where should 
>> I go?
>> What questions should I  ask?
> 
> Semantic web technologies can help make certain things simpler to 
> implement -- and therefore allow things to be implemented that would not 
> have been feasible otherwise. But tasks such as listing all proteins for 
> an organism that have been tagged with a specific term are simple enough 
> to be supported even without any semantic web magic, see 
> http://pir.uniprot.org/, for example. This site also allows you to run 
> similarity searches on the matching entries to find homologs.
> 
> Now in this particular case it looks like you are out of luck: No yeast 
> proteins have been associated with GO:0031930. Often the main limiting 
> factor are not the tools, but the available data...
> 

There are S. cerevisiae proteins assigned to GO:0031930 though, you can 
see them here: <http://tinyurl.com/d2dm9>

The next step would be to take the sequences from those identified 
proteins (which are supplied in FASTA format) and run a BLAST search 
with each to identify sequence homologues 
<http://pir.uniprot.org/search/blast.shtml>.

Alternatively, you could follow the 'SGD' link from alongside each 
protein in GO, then use the 'PDB homologs' link from the bottom of the 
summary page or one of the 'Comparison Resources' tools on the 
right-hand side to find homologues.

alf.
Received on Tuesday, 31 January 2006 20:58:38 GMT

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