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MvirDB


NAR Molecular Biology Database Collection entry number 996
Zhou C.E.Z., Smith J., Lam M.W., Zemla A.T., Dyer M. and Slezak T.

Database Description

MvirDB (http://mvirdb.llnl.gov/) is a microbial data warehouse of protein toxins, virulence factors, and antibiotic resistance genes for bio-defense applications. MvirDB integrates all publicly available, organized sequence data for protein toxins, virulence factors, and antibiotic resistance genes into a single database, which is easy to access, and which provides value-added annotation information of particular use in bio-defense and medical applications. MvirDB integrates DNA and protein sequence information from several data sources: Tox-Prot, SCORPION, the PRINTS database of 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 (MannDB) and is linked to that system’s browser tool for convenient display of annotation results. We expect to update MvirDB soon to include lists of hand-compiled known virulence factors from the literature and entries from the Snake neurotoxin database, MOLLUSK, and Conotoxins.

Acknowledgements

Construction of MvirDB was performed under the auspices of the U.S. Department of Energy by the University of California Lawrence Livermore National Laboratory under contract no. W-7405-ENG-48 and was supported by funding from the Department of Homeland Security.

References

1. Alba,M.M., Lee,D., Pearl,F.M.G., Shepherd,A.J., Martin,N., Orengo,C.A., and Kellam,P. (2001) VIDA: a virus database system for the organization of animal virus genome open reading frames. Nucleic Acids Res., 29, 133-136.
2. Attwood,T.K., Bradley,P., Flower,D.R., Gaulton,A., Maudling,N., Mitchell,A.L., Moulton,G., Nordle,A., Paine,K., Taylor,P., Uddin,A., and Zygouri,C. (2003) PRINTS and its automatic supplement, preprints. Nucleic Acids Res., 31, 400-402.
3. Chen,L., Yang,J., Yu,J., Yao,Z., Sun,L., Shen,Y., and Jin,Q. (2005) VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res., 33: D325-D328.
4. Jungo,F. and Bairoch,A. (2005) Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase. Toxicon, 45, 293-301.
5. Mantri,Y. and Williams,K.P. (2004) Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities. Nucleic Acids Res., 32, D55-D58.
6. Scaria,J., Ghandramouli,U., and Verma,S.K. (2005) Antibiotic resistance genes online (ARGO): A database on vancomycin and b-lactam resistance genes. Bioinformation, 1, 5-7.
7. Srinivasan,K.N., Gopalakrishnakone,P., Tan,P.T., Chew,K.C., Cheng,B., Kini,R.M., Koh,J.L.Y., Seah,S.H., and Brusic,V. (2001) SCORPION, a molecular database of scorpion toxins. Toxicon, 40, 23-31.


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