This release of TVFac was built using Integr8 version 100 (released on Sep 22, 2009 using UniProt version 15.8) and includes 5.9 million proteins from 1422 Bacteria, 70 Archaea, and 80 Eukaryotic genome sequencing projects (1572 total). Updates are planned for every fifth release of Integr8. If you have any questions or comments about this website, please send an email to Chris Stubben (stubben at lanl dot gov)
Brief History: The Toxin and Virulence Factor (TVFac) database was originally designed to annotate toxins
and virulence factors in 2001. Due to the rapid growth in genome sequencing projects, we no longer annotate
virulence genes; instead we search Gene Ontology and other database
annotations in UniProt and the NIAID-funded
Bioinformatic Resource Centers to
identify adhesion factors, invasins, secretion systems, toxins, antibiotic resistance genes, and other virulence factors.
Phylogenetic profiles were one of many tools available in early releases of TVFac and were used to identify virulence-related proteins. A link to the profile tables created in 2005 using BLAST clusters is still available. These tables were created by downoading proteins from all microbial genomes (214 total), running all vs. all protein BLAST, and then clustering the results at different percent identify and query coverage cutoffs. The BLAST-based clusters were soon replaced by UniRef clusters and cross-references in the UniProt database. These profile tables are created by parsing the annotation in UniProt files, loading the results into a MySQL database, and then running cross-tabulations to summarize the hits by genome project into the profile table format.
