To generate genome-wise orthologs including paralogs from OMA

Question

[mzzzzzzzzzz]

Hi, I'm new to homology and OMA. In my project, I would like to generate the whole genome homology between different individuals of the same species. I have assembled 3 different individuals genome, and also generated their annotation. Now I ran OMA standalone to estimate the homology between these individuals together with several sister species downloaded from OMA database. I found that the resulted file 'OrthologousGroups.txt ' for OMA group is very useful, and it's what I would like to have, despite that it's lacking the paralogy information.

So my goal is to get a homology group gene list from HOG information. I have checked the OMA primer instruction and pyham instruction , and I still didn't figure out how I can generate a list of genes of HOG. Meanwhile, I checked the HOGFasta folder in the output of OMA, and notice that each HOG has its own fast file that includes all the homologous genes.

So my questions are : (1) Can I just simply list all the gene names in each HOG fasta file to get the homology gene list? If I understand correctly of OMA, paralogs has their own HOG number, right? (2) If the (1) gets a NO, then how shall I generate the homology gene list? Could you give me some hints here?

Thanks a lot!

Answer 1

[Adrian Altenhoff]

Hi mzzzzzzzzzz

Sorry for the slow reply.

yes, the HOGFasta folder contains one fasta file for each root HOG. It contains all the proteins that belong to the same homologous group (starting with a speciation event). So it is as close as we can get to the list of homologs with from the OMA output. If genes duplicated within this family, you will find both copies in the OMAFasta file.

Best wishes Adrian