FEMS Microbiol Lett. 2003 Aug 29;225(2):213-20.

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

Charlebois RL, Clarke GD, Beiko RG, St Jean A.

Source

NeuroGadgets Inc., www.neurogadgets.com, Ottawa, Ontario, Canada. rlcharlebois@neurogadgets.com

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.

PMID:: 12951244; [PubMed - indexed for MEDLINE]

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