Orthologs In Orthomcl

Question

[figo]

Hi All,

I ran the orthomcl between two species and now i am getting an pair of orthologs like this(example):

E278 m.102244 1.039 E278 m.102246 1.039 E278 m.102248 1.039 E282 m.40012 1.039 E282 m.40016 1.039 E282 m.40018 1.039 E290 m.46499 1.039 E294 m.103490 0.563

Now i want to ask that the first column is the 1st species and 2nd columns is the second species. But in first columns many of the ids are same like E278 and have different hits. I can understand those can be the isoforms.Also the similar is if i see the second columns there are species have more than one hit. So I want to know how i can get exact orthologs from the orthomcl.

regards

[Irsan]

Is your question just a file-processing question where you want to get the unique IDs in either column A or B? Or is it more general like "How can I get a list of all orthologuous gene pairs in species A and species B. And why do you use orhomcl (why not Biomart)? Do the orthouloguous gene pairs have to be a specific functional groups like "ubiquitin conjugating enzyme" (that is what orthocml seems to be useful for)

[figo]

Than you for your reply. I just wanted to know that if you get more then one ortholog for a gene than what can be reason for that as this can be 1 to many relationship of orthologous. But then some how i loose the 1:many orthologous genes for further analysis say a positive selection test there i need to have a strict orthology and when i have many orthologs then i cannot use that gene.Is there a way i can use to get those genes in picture so that i can maximize my number of orhtologs between the species.

Answer 1

[miquelduranfrigola]

Hi Figo,

when you say "exact orthologs", what do you mean? 1-to-1 relationship? Also, I do not see why repeated IDs should correspond to isoforms (maybe yes, but this can also be the way a one-to-many relationship is displayed in column format).

You might also want to try out OMA. Maybe it fits your needs.

[figo]

First thanks for your reply and i am copying the same from the top comment which i did : I just wanted to know that if you get more then one ortholog for a gene than what can be reason for that as this can be 1 to many relationship of orthologous. But then some how i loose the 1:many orthologous genes for further analysis say a positive selection test there i need to have a strict orthology and when i have many orthologs then i cannot use that gene.Is there a way i can use to get those genes in picture so that i can maximize my number of orhtologs between the species.