title: Characterization of species-specific genes using a flexible, web-based querying system.
abstract: We describe a query-based web-accessible system (www.neurogadgets.com/bws.php) for facilitating comparative microbial genomics. A variety of query pages are available, each with numerous options, that allow a biologist to pose relevant questions of genomic data. We illustrate with a characterization of species-specific protein-coding genes (so-called "ORFans"), finding that they are on average smaller, faster evolving, and less G+C-rich, and that they encode proteins more basic in their predicted isoelectric point, compared with non-species-specific genes. Using a dual-threshold approach, we conclude that these are characteristics of true species-specific genes, rather than artifacts of mis-annotation.
authors.affiliation: NeuroGadgets Inc., www.neurogadgets.com, Ottawa, Ontario, Canada. rlcharlebois@neurogadgets.com
authors.forename: Robert L
authors.initials: RL
authors.lastname: Charlebois
authors.forename: G D Paul
authors.initials: GD
authors.lastname: Clarke
authors.forename: Robert G
authors.initials: RG
authors.lastname: Beiko
authors.forename: Andrew
authors.initials: A
authors.lastname: St  Jean
mesh_terms: D001482:Base Composition; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D005827:Genetics, Microbial; D023281:Genomics; D020407:Internet; D016366:Open Reading Frames; D013045:Species Specificity