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Question: OMA - without all vs all
1
gravatar for dtejadamartinez
12 months ago by
dtejadamartinez • 10
dtejadamartinez • 10 wrote:

I have a data set of 700 coding sequences (which I saved in a reference.fa file) and I need to obtain the orthology relationships (orthologous and paralogous) of these genes against 70 species. I have downloaded the genome cds from NCBI for each species. Now, is it possible to get only these comparisons without going through the all vs all phase? Could I start OMA without comparing all the genomes (cds) with each other? How do I launch these analyses ?

Thanks for your help,

orthology oma • 428 views
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modified 12 months ago • written 12 months ago by dtejadamartinez • 10

Thanks for your help,

I think I would compute all vs all then.

ADD REPLY • link written 12 months ago by dtejadamartinez • 10
0
gravatar for Christophe Dessimoz
12 months ago by
Christophe Dessimoz • 500
University College London
Christophe Dessimoz • 500 wrote:

At the moment, it’s necessary to compute all-all among your 70 genomes as well to elucidate orthology relationships.

However, I see two fast alternatives:

1) If these 70 reference genomes are available in OMA, you could export them including all-against-all. Then, OMA would “just” need to compute the 700 CDS against the 70 genomes (and the CDS against themselves but that would be very fast.)

2) if you are mainly interested in functional annotation, you could use the new annotation feature of the OMA browser (https://omabrowser.org/oma/functions/). There is also a REST API function for that (https://omabrowser.org/api/docs#function)
ADD COMMENT • link modified 12 months ago • written 12 months ago by Christophe Dessimoz • 500
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