title: MvirDB--a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications.
abstract: Knowledge of toxins, virulence factors and antibiotic resistance genes is essential for bio-defense applications aimed at identifying 'functional' signatures for characterizing emerging or engineered pathogens. Whereas genetic signatures identify a pathogen, functional signatures identify what a pathogen is capable of. To facilitate rapid identification of sequences and characterization of genes for signature discovery, we have collected all publicly available (as of this writing), organized sequences representing known toxins, virulence factors, and antibiotic resistance genes in one convenient database, which we believe will be of use to the bio-defense research community. MvirDB integrates DNA and protein sequence information from Tox-Prot, SCORPION, the PRINTS virulence factors, VFDB, TVFac, Islander, ARGO and a subset of VIDA. Entries in MvirDB are hyperlinked back to their original sources. A blast tool allows the user to blast against all DNA or protein sequences in MvirDB, and a browser tool allows the user to search the database to retrieve virulence factor descriptions, sequences, and classifications, and to download sequences of interest. MvirDB has an automated weekly update mechanism. Each protein sequence in MvirDB is annotated using our fully automated protein annotation system and is linked to that system's browser tool. MvirDB can be accessed at http://mvirdb.llnl.gov/.
authors.affiliation: Pathogen Bioinformatics, Mailstop L-174 Energy, Environment, and Biology Division, Computations Directorate, Lawrence Livermore National Laboratory, 70000 East Avenue, Livermore, CA 94550, USA. zhou4@llnl.gov
authors.forename: C E
authors.initials: CE
authors.lastname: Zhou
authors.forename: J
authors.initials: J
authors.lastname: Smith
authors.forename: M
authors.initials: M
authors.lastname: Lam
authors.forename: A
authors.initials: A
authors.lastname: Zemla
authors.forename: M D
authors.initials: MD
authors.lastname: Dyer
authors.forename: T
authors.initials: T
authors.lastname: Slezak
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics; D001427:Bacterial Toxins / Q000737:chemistry / Q000235:genetics; D023482:Bioterrorism; D030541:Databases, Genetic; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D020407:Internet; D017422:Sequence Analysis, DNA; D020539:Sequence Analysis, Protein; D014118:Toxins, Biological / Q000737:chemistry* / Q000235:genetics*; D014584:User-Computer Interface; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics; D037521:Virulence Factors / Q000737:chemistry* / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D001427:Bacterial Toxins; D014118:Toxins, Biological; D014764:Viral Proteins; D037521:Virulence Factors