Reciprocal (Multiple-way) Best BLAST Hits
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10 weeks ago
Junior • 0

I have protein sequences in five fasta files from species A, B, C, D and E. I want to select 500 genes from species A that meet the following criterion: have five-way best BLAST hits between species A, B, C, D and E;

I have found some scripts to handle one-way; however, I have been trying to get information for multiple-way.

I will appreciate any assistance with any guidelines, program and scripts suggestions.

Thank you in advance.

Blast orthologs • 463 views
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This sounds quite specific, so you'll probably need to write your own scripts to parse BLAST outputs. If you can't code, then try to get help from a bioinformatician. You may also want to look into sequence clustering methods like CD-HIT (very simple) or OrthoFinder2 (more sophisticated).

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Perhaps I should mention that I only need helps for the first criterion. I will edit my post.

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Do you have to use reciprocal best blast hits for this?

liorglic's suggestion to use something like OrthoFinder is likely to give you a better result than blast alone.

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Hey, liorglic and Dave.

Yes, I have considered using OrthoFinder2.

However, from what I have understood, it identifies orthologs in a pairwise manner (i.e specie1_vs_species2).

So if I provide three species (1, 2 and 3), I will not be able to get a 3-way identified orthologs.

Or is there an option in OrthoFinder to get a multiple-way identified orthologs?

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Yes, you can use Orthofinder for multiple species/samples.

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You misunderstood. OF2 will produce clusters for multiple species, not just pairwise orthologs (this is the whole idea of clustering...)

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