How to find the true orthologs from recipocal blast hits (blastn) ?

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3.7 years ago

sunnykevin97 ▴ 990

Hi,

After recipocal blast (blastn) analysis, from 7 different species, I got a ~10,000 orthologs as a final set. How do I find the true orthologs from the final set ?

Suggestions please!

Thanks

RNA DNA blast alignment • 1.2k views

ADD COMMENT • link 2.4 years ago by sunnykevin97 ▴ 990

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Without phylogeny analysis there is a high error rate, but using MCL like OrthoMCL could probably help.

ADD REPLY • link 3.7 years ago by Juke34 8.9k

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Have you tried using databases of orthologous proteins like COG or EggNOG? The problem of assigning orthology groups is not simple at all.

ADD REPLY • link 3.7 years ago by Asaf 10k

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Have you look at OrthoFinder2?

ADD REPLY • link 3.7 years ago by Juke34 8.9k

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Yes, I already did the analysis. Orthogroups_for_concatenated_alignment.txt file shows 1088 sequences. Can I consider these as orthologs ?

Or else, which folder/files do I consider the orthologs sequences ?

Thanks Kevin.

ADD REPLY • link 3.7 years ago by sunnykevin97 ▴ 990

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