Cross Species Orthologues

Question

[Apricimo]

Hello all,

I want to compare protein (amino acid) sequences of two organisms on a genome scale. That is, if I have organism A with 10 proteins (hypothetical) and another organism B with 10 proteins I would like to see what proteins in B are orthologues to A based on sequence identity/similarity. Theoretically where I can tabulate the results as follows.

Protein from A   |    Protein from B and  Identity to A
1                |    4                   80%
2                |    1                   45%
3                |    10                  30%
4                |    ---                 No orthologue
5                |    9                   65%

etc.

I guess my question is what tools are out there to do this on a large scale not just one by one through NCBI blast.

Thank you

Answer 1

[h.mon]

A simple (and naive) way of doing this is performing BLAST searches of one proteome against the other and picking reciprocal best hits, filtering in some way - percent identity or e-score.

There are several programs which perform ortholog searches, OrthoMCL and OMA being two widely used choices.

Answer 2

[dago]

Look into Biostars, there are many similar posts: Ortholog Protein Finding Tool

Answer 3

[Apricimo]

This is exactly the kind of thing I needed.

http://omabrowser.org/oma/genomePW/

Preferred ID is to use protein names used by kegg "Source ID"