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Identify Common Orthologs In 3 Genome

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.

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updated by cdsouthan cdsouthan • written by prp491 • prp491

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

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written by JC JC

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.

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written by colinDotAIBN • colinDotAIBN

4 answers

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.

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written by lh3 lh3

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.

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written by JC JC

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

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written by prp491 • prp491

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.

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written by JC JC

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

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written by Rahul Sharma Rahul Sharma

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

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written by prp491 • prp491

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

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written by cdsouthan cdsouthan

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