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 detect missing 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 standalone, downloadable package, requiring only a set of GenBank annotation files as input. The software automatically generates a homology structure using reciprocal BLAST and a synteny-based method; 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 and Ka is the number of nonsynonymo

SUBMITTER: Oheigeartaigh SS 

PROVIDER: S-EPMC4010983 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature