synder: inferring genomic orthologs from synteny maps

Abstract

AbstractOrtholog inference is a key step in understanding the evolution and function of a gene or other genomic feature. Yet often no similar sequence can be identified, or the true ortholog is hidden among false positives. A solution is to consider the sequence’s genomic context. We present the generic program,synder, for tracing features of interest between genomes based on a synteny map. This approach narrows genomic search-space independently of the sequence of the feature of interest. We illustrate the utility ofsynderby finding orthologs for theArabidopsis thaliana13-member gene family of Nuclear Factor YC transcription factor across the Brassicaceae clade.