Which tools to group orthologous proteins?

Question

[biolab]

Hi everyone

I have many protein sequences from new species. The data for these species is more complete than those collected in Genbank db. I would like to group orthologous proteins into clusters. Which tools can be applied for this work? I very appreciate your advice. Thank you greatly!

[shelly.deforte]

This may not be what you're looking for, but I like to do rough sequence clustering on my protein sets using CD-hit. It's very fast and can give you an idea of your protein demographics. This is what UniProt uses to cluster.

[biolab]

Thank you for your comment that is very helpful.

Answer 1

[dago]

Look here, maybe it helps: Detecting unique genes or non-homologus genes in a species

[pld]

BRBH is a great way to establish orthologous genes, but this process can become computationally difficult if you are working with eukaryotic species.

OP, you should still take the currently available annotations into consideration. They can serve as sanity checks and you may be able to correct problems in whatever is currently available.

[biolab]

Thanks, joe.cornish826. Your advices is helpful!

[biolab]

Thanks a lot, dago. I want to ask you one more question. The methods in OrthoMCL and InParanoid are a little bit complicated (OMCL needs mysql and other tools). I want to use reciprocal best-hit BLAST approach, the simplest method. But after BLAST, is there any perl script to group orthologous proteins? THANKS!

[biolab]

Hi, dago, I downloaded get_homoilogous. Let me try it. THANKS!