Given 3 FASTA files, how can I find putative orthologs?
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5.9 years ago

I have the CDS FASTA files for 3 organisms. I was wondering if there was a quick script, set of online tools, or methods to find the 3-way orthologs between these 3 organisms using the CDS FASTA files? 

ortholog genome • 1.7k views
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5.9 years ago
h.mon 33k

There are loads of options. For example, OMA and OrthoMCL are two popular software. You can look at MCL page under protocols for a quick how-to on clustering blast results - probably the simplest solution for you. You could also read old posts for suggestions, e.g. here and here.

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To use OMA on your own fasta files, use the standalone version here: http://omabrowser.org/standalone

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5.9 years ago
Adrian Pelin ★ 2.5k

For just 3, I would use inparanoid, it does pairwise comparisons:

http://software.sbc.su.se/cgi-bin/request.cgi?project=inparanoid

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