A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes

We present a hidden Markov model based approach we call delta-bitscore (DBS) for identifying orthologous proteins that have diverged at the amino acid sequence level in a way that is likely to impact biological function. We benchmark this approach with several widely used datasets and apply it to a proof-of-concept study of orthologous proteomes in an investigation of host adaptation in Salmonella enterica. We highlight the value of the method in identifying functional divergence of genes, and suggest that this tool may be a better approach than the commonly used dN/dS metric for identifying functionally significant genetic changes occurring in recently diverged organisms.
Availability and Implementation: A program implementing DBS for pairwise genome comparisons is freely available at: https://github.com/UCanCompBio/deltaBS.
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Supplementary information: Supplementary data are available at Bioinformatics online.

Source: Bioinformatics - November 28, 2016 Category: Bioinformatics Authors: Wheeler, N. E., Barquist, L., Kingsley, R. A., Gardner, P. P. Tags: SEQUENCE ANALYSIS Source Type: research