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/.

Figure 1

Dataflow diagram for MvirDB. Public-access and proprietary data sources are downloaded and parsed into MvirDB. Protein entries in MvirDB are sorted by organism type (e.g. Gram-positive bacterium, eukaryotic virus) and annotated using the MannDB automated annotation system. Additional links are established between MvirDB and MannDB when entries contain common external database identifiers. Web client browser and BLAST interfaces enable viewing and analysis of data.

Figure 2

Virulence database browser sample web pages. An example free-text query on ‘Outer membrane’ yields 203 entries from VFDB, TVFAC and PRINTS data sources. User can then select a virulence factor (e.g. 10 963; center panel) and display a sequence (lower right panel). Linking from the sequence display page via the virulence database entry ID displays external database cross-reference IDs (lower left panel).