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Nucleic Acids Research Advance Access originally published online on November 7, 2006
Nucleic Acids Research 2007 35(Database issue):D391-D394; doi:10.1093/nar/gkl791
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Nucleic Acids Research, 2007, Vol. 35, Database issue D391-D394
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

MvirDB—a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications

C. E. Zhou*, J. Smith, M. Lam, A. Zemla, M. D. Dyer1 and T. Slezak

Pathogen Bioinformatics, Mailstop L-174 Energy, Environment, and Biology Division, Computations Directorate, Lawrence Livermore National Laboratory, 70000 East Avenue, Livermore, CA 94550, USA 1 Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University Blacksburg, VA, USA

*To whom correspondence should be addressed. Tel: +1 925 422 2117; Fax: +1 925 423 6437; Email: zhou4{at}llnl.gov

Received June 5, 2006. Revised August 28, 2006. Accepted October 2, 2006.

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/.


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