OMA - without all vs all

Question

[dtejadamartinez]

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,

[dtejadamartinez]

Thanks for your help,

I think I would compute all vs all then.

Answer 1

[Christophe Dessimoz]

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)

[ilenia.urso]

I am trying to run OMA (version OMA.2.4.2) on cluster using SLURM. I basically followed the procedure described in Oma Cheat Sheet, and in my DB directory I collected genomes for 20 species (coming from OMA using the export option) plus the genome of my species of interest. However, the array-job (splited into 1000 parallelized jobs) seems to take a lot of time (each job runs for over 8 hours!) Is there any way to speed up this step?

Thank you, Ilenia