Question: Can OMA calculate orthologs for single query sequence?
2
gravatar for a.zielezinski
22 months ago by
a.zielezinski7.4k
a.zielezinski7.4k wrote:

Is it possible to search for orthologs/inparalogs only for specific sequences in the query genome?

I'm aware that searching for orthologs requires complete proteomes. I would like to avoid a step where OMA calculates all-versus-all sequence comparisons of all proteins from query and subject genomes. In fact, I don't have to BLAST all proteins in a proteome when I'm interested only in one protein. I was wondering whether OMA can be used this way? For example, Reciprocal Smallest Distance (RSD) approach lets users to find orthologs for specific sequences in the query genome.

 

 

ortholog oma standalone • 883 views
ADD COMMENTlink modified 22 months ago by cyril-cros800 • written 22 months ago by a.zielezinski7.4k
4
gravatar for Christophe Dessimoz
22 months ago by
University College London
Christophe Dessimoz410 wrote:

If your specific sequence is part of a genome in the OMA database, it is of course possible to retrieve the inferred orthologs for this sequence only. For this, use the search function with an identifier or the sequence itself.

If the sequence is not in OMA, you can export a few closely related genomes and run the OMA standalone on them and your sequence. Assuming that the genomes are somewhat complete, the orthologs inferred for your sequence should be fairly reliable. Thanks to the reciprocal criterion (roughly the RSD criterion you mention) and the use of "witnesses of non-orthology", things only start to fall apart when most genomes are very incomplete. 

ADD COMMENTlink modified 22 months ago • written 22 months ago by Christophe Dessimoz410
1
gravatar for cyril-cros
22 months ago by
cyril-cros800
France
cyril-cros800 wrote:

You have a very large many number of databases with precomputed groups of orthologs. Try http://orthodb.org/ which is quite complete.
Another technique is to look at genes in the vicinity of your protein, they may be part of a synteny group.

ADD COMMENTlink written 22 months ago by cyril-cros800
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 962 users visited in the last hour