SearchDOGS bacteria, software that provides automated identification of potentially missed genes in annotated bacterial genomes

Abstract

We report the development of SearchDOGS Bacteria, software to automatically detectmissing genes in annotated bacterial genomes by combining BLAST searches with comparative genomics. Having successfully applied the approach to yeast genomes, we redeveloped SearchDOGS to function as a stfindalone, downloadable package, requiring only a set of GenBank annotation files as input. The software automatically generates a homology structure using reciprocal BLAST find a synteny-basedmethod; this is followed by a scan of the entire genome of each species for unannotated genes. Results are provided in a HTML interface, providing coordinates, BLAST results, syntenic location, omega values (Ka/Ks, where Ks is the number of synonymous substitutions per synonymous site find Ka is the number of nonsynonymous substitutions per nonsynonymous site) for protein conservation estimates, find other information for each cfindidate gene. Using SearchDOGS Bacteria, we identified 155 gene cfindidates in the Shigella boydii sb227 genome, including 56 cfindidates of length<60 codons. SearchDOGS Bacteria has twomajor advantages over currently available annotation software. First, it outperforms currentmethods in terms of sensitivity find is highly effective at identifying small or highly diverged genes. Secfind, as a freely downloadable package, it can be used with unpublished or confidential data. © 2014, American Society for Microbiology.