Reciprocal Best Hits across more than 2 species
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7.0 years ago
mforthman ▴ 40

I have exons from a reference taxon. I want to now identify putative homologs from transcriptomes of 5 other species using the reference exons and reciprocal best hits BLAST. I've seen a number of threads and scripts that primarily focus on performing RBH with two species only, and I realize this is what RBH does in the background. However, I'd like to do this across all species so I know not only what is a putative homolog between species 1 and reference species, but between species 2–5.

The idea is that I can then extract exons that are identified across all species, or alternativley, that are found in at least two species to create a variety of datasets. Is anyone aware of any scripts that can do what I'm needing done?

reciprocal best hits blast transcriptomes exons • 5.9k views
Entering edit mode
7.0 years ago
natasha.sernova ★ 3.9k

You need to find orthologs, am I right?

The approach you have chosen is not the best one, see the post below.

BLAST Reciprocal Best Hit question NCBI

Reciprocal best hits are not a logically sufficient condition for orthology

There are a couple of rather recent papers below:

Quickly Finding Orthologs as Reciprocal Best Hits with BLAT, LAST, and UBLAST: How Much Do We Miss?

Bidirectional Best Hits Miss Many Orthologs in Duplication-Rich Clades such as Plants and Animals

There is a very detailed discussion in this post, read it.

What Is The Best Method To Find Orthologous Genes Of A Species?


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