Abstract
CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R
Highlights
SummaryCRBHits is a coding sequence (CDS) analysis pipeline in R (R Core Team, 2019)
The Reciprocal Best Hit (RBH) approach is commonly used in bioinformatics to show that two sequences evolved from a common ancestral gene
The initial sequence search step is classically performed with the Basic Local Alignment Search Tool (Altschul et al, 1990) and due to evolutionary constraints, in most cases protein coding sequences are compared between two species
Summary
CRBHits is a coding sequence (CDS) analysis pipeline in R (R Core Team, 2019). It reimplements the Conditional Reciprocal Best Hit (CRBH) algorithm crb-blast and covers all necessary steps from sequence similarity searches, codon alignments to Ka/Ks calculations and synteny. Downstream analysis use the resulting RBH to cluster sequence pairs and build so-called orthologous groups like e.g. OrthoFinder (Emms & Kelly, 2015) and other tools. As described earlier (Aubry et al, 2014; Scott, 2017), CRBH uses the sequence search results to fit an expect value (E-value) cutoff given each RBH to subsequently add sequence pairs to the list of bona-fide orthologs given their alignment length.
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