Reciprocal (Multiple-way) Best BLAST Hits

Question

[Junior]

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.

[liorglic]

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).

[Junior]

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

[Dave Carlson]

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.

[Junior]

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?

[Buffo]

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

[liorglic]

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