Identify Common Orthologs In 3 Genome

Question

[prp491]

I have 3 genomes A, B and C. I want to identify the common and unique orthologs among these genomes. can anyone suggests an window OS based solution please.

[JC]

I deleted your PLZZZ, please write correctly if you want a serious response to your question.

[colinDotAIBN]

The relatedness of the organisms is also important. Some programs work better for closely related organisms, while others work better for organisms that are spread across kingdoms.

Answer 1

[lh3]

If by "unique orthologs", you mean 1:1 orthologs, it is simple: between each pair of genomes, find the reciprocal best blast hits (the best hit to gene A in species 1 is gene B in species 2 and vice versa) and then combine them. Finding non 1:1 orthologs is much harder.

Answer 2

[JC]

If your species are in Ensembl, a simple solution is obtaining the list of orthologs using Compara API or BioMart. Otherwise you will need to search them, you can use a bi-directional blast approach like the one described here.

[prp491]

but what if i have 3 genomes. i am little bit confused. My genomes are not in Ensembl

[JC]

you need to do the analysis in pairs, A-B, B-C and A-C, then simply combine the lists looking for the core genes shared between the 3 species, and unique genes in each set.

Answer 3

[Rahul Sharma]

Hi, I did the same analysis on four species, used OrthoMCL software. and shell commands for 1:1 relationships. Please try to install and use OrthoMCL on unix based system. It is very easy and fast. Regards, Rahul

[prp491]

I know about OrthoMCL but I was looking for window alternatives. However thanks rahul

Answer 4

[cdsouthan]

Unless you have some estimate of divergence time the exercise may not that informative anyway