Identification Of Orthologus Genes

Question

[Adarsh Kuamr]

hiii,, there is any software by which we directly identify orthologus genes in different animals. thanks you.

[Fabian Bull]

Could specify what kind of data you have? What is your background?

Answer 1

[Duff]

The question is vague. Here is starting point perhaps:

http://www.ensembl.info/blog/2009/01/21/how-to-get-all-the-orthologous-genes-between-two-species/

Best

d

Answer 2

[Larry_Parnell]

You should review the fine answers posted to this very similar question on BioStar. This includes traditional as well as newer, less conventional views of what constitutes an ortholog and how to identify such.

Answer 3

[DG]

Larry's advice to check out the answers in the other similar question is good. But I will point out (and made a comment there) that lineage specific duplications can make the pure phylogenetic method tricky. If inparalogs and coorthologs are present doing ortholog identification can be a little bit of a black art.

I'm a big fan of OrthoMCL, if you can set that up locally you can run it on your complete genomes and it will identify Paralogs, Orthologs, Inparalgs, and Coorthologs.

[lh3]

Pure phylogenetic methods are designed to fully address inparalogs. Most inparalogs can be identified quite accurately with modern methods. They are not black art at all. What is more of an issue is incomplete lineage sorting and lateral gene transfer (in prokaryotes).

[lh3]

Pure phylogenetic methods are designed to fully address inparalogs. Most inparalogs can be identified quite accurately with modern methods. They are not black art at all. What is more of an issue are incomplete lineage sorting and lateral gene transfer (in prokaryotes).