GenomegaMap: Within-Species Genome-Wide dN/dS Estimation from over 10,000 Genomes.

ABSTRACT: The dN/dS ratio provides evidence of adaptation or functional constraint in protein-coding genes by quantifying the relative excess or deficit of amino acid-replacing versus silent nucleotide variation. Inexpensive sequencing promises a better understanding of parameters, such as dN/dS, but analyzing very large data sets poses a major statistical challenge. Here, I introduce genomegaMap for estimating within-species genome-wide variation in dN/dS, and I apply it to 3,979 genes across 10,209 tuberculosis genomes to characterize the selection pressures shaping this global pathogen. GenomegaMap is a phylogeny-free method that addresses two major problems with existing approaches: 1) It is fast no matter how large the sample size and 2) it is robust to recombination, which causes phylogenetic

SUBMITTER: Wilson DJ 

PROVIDER: S-EPMC7403622 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature