Characterization of species-specific genes using a flexible, web-based querying system

• Published in: FEMS microbiology letters Vol. 225; no. 2; pp. 213 - 220
• Main Authors: Charlebois, Robert L, Clarke, G.D.Paul, Beiko, Robert G, St. Jean, Andrew
• Format: Journal Article
• Language: English
• Published: Oxford, UK Elsevier B.V 29.08.2003; Blackwell Publishing Ltd; Blackwell
• Subjects: Bacteriological methods and techniques used in bacteriology; Bacteriology; Base Composition; Biological and medical sciences; Computational Biology - methods; Databases, Genetic; Fundamental and applied biological sciences. Psychology; Genetics; Genetics, Microbial; Genomics; Internet; Microbial evolution; Microbial genomics; Microbiology; NGIBWS; Open Reading Frames; ORFan; Species Specificity; Species-specific genes; Species-specific genes; Microbial genomics; NGIBWS; Microbial evolution; ORFan; Characterization; Procaryote; Gene; Genomics; Bacteria; Species specificity; Internet; Comparative study
• ISSN: 0378-1097; 1574-6968
• DOI: 10.1016/S0378-1097(03)00512-3

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.