Characterization of species-specific genes using a flexible, web-based querying system.
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.
Charlebois
Robert L
RL
NeuroGadgets Inc., www.neurogadgets.com, Ottawa, Ontario, Canada. rlcharlebois@neurogadgets.com
Clarke
G D Paul
GD
Beiko
Robert G
RG
St  Jean
Andrew
A
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