| Hi, I thought this might be a good place to advertise our new tool: Genome Annotation Transfer Utility (GATU) We developed it because we found ourselves annotating lots of viral genomes for which there was a close relative already annotated (eg SARS). Our paper (below) also describes results using it on bacterial genomes. Essentially, GATU takes the proteins/mature peptides of the reference genome and BLASTs against the genome to be annotated in order to find already known genes. It also finds novel ORFs, unique in the target genome - and allows further analysis. It's not a gene predictor, but we've found that it can annotate >90% of genes without intervention and allows the user to keep control over selection of genes to be annotated. The end product is a GenBank file. See: Tcherepanov VT, Ehlers A, Upton C. (2006) Genome Annotation Transfer Utility (GATU): Rapid annotation of viral genomes using a closely related reference genome. BMC Genomics. 2006 Jun 13;7(1):150 Questions welcome! Also check out http://www.biodirectory.com/uptons_blog.html Chris Upton
Biochemistry and Microbiology Tel. 250-721-6507 University of Victoria Fax 250-721-8855 P.O. Box 3055 STN CSC Victoria, BC V8W 3P6 Canada
web.uvic.ca/~cupton www.virology.ca http://www.biodirectory.com/uptons_blog.html
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