ortholog finding with unsequenced species

Question

[Mehmet]

Hi

I have protein files of two non-model and newly sequenced species, and I want to find orthologs among species, which are relatively close and far to my species (ex. share same habitat, host etc.). I can access some species that I want to use for searching orthologs like C. elegans. But some species which have not been sequenced yet or of which protein data is not available, except some gene sequences. How workflow should I follow?

Answer 1

[Antonio R. Franco]

You need to run BLAST searches with public and also with local databases

[Mehmet]

Hi,

I am using OrthoMCL tool to find orthologs and then I will make phylogenetic tree using orthologs. I am trying to use different species for this. So far, I have been able to find C. elegans, some other species` protein file, which have been sequenced completely. To use protein files in OrthoMCL, I need completely sequenced species` file.

Answer 2

[Antonio R. Franco]

Use Blast and local Blast. They do a nice work in finding orthologs

With local Blast you can set your own databases, and don't need to be a whole organism genome's

A Google search make the magic of telling you how to do it. It is pretty easy