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

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          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/.

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          Most cited references10

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          PRINTS and its automatic supplement, prePRINTS.

          The PRINTS database houses a collection of protein fingerprints. These may be used to assign uncharacterised sequences to known families and hence to infer tentative functions. The September 2002 release (version 36.0) includes 1800 fingerprints, encoding approximately 11 000 motifs, covering a range of globular and membrane proteins, modular polypeptides and so on. In addition to its continued steady growth, we report here the development of an automatic supplement, prePRINTS, designed to increase the coverage of the resource and reduce some of the manual burdens inherent in its maintenance. The databases are accessible for interrogation and searching at http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/.
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            Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities.

            Prokaryotic chromosomes often contain islands, such as temperate phages or pathogenicity islands, delivered by site-specific integrases. Integration usually occurs within a tRNA or tmRNA gene, splitting the gene, yet sequences within the island restore the disrupted gene. The regenerated RNA gene and the displaced fragment of that gene thus mark the endpoints of the island. We applied this principle to search for islands in genomic DNA sequences. Our algorithm generates a list of tRNA and tmRNA genes, uses each as the query for a BLAST search of the starting DNA and removes unlikely hits through a series of filters. A search for islands in 106 whole bacterial genomes produced 143 candidates, with the search itself providing an estimate of three false candidates among these. Preliminary phylogenetic analysis of the associated integrases reduced this set to 89 cases of independently evolved site specificity, which showed strong bias for the tmRNA gene. The website Islander (http://www.indiana.edu/ approximately islander) presents the candidate islands in GenBank-style files and correlates integrase phylogeny with site specificity.
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              Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase.

              The Tox-Prot program was initiated in order to provide the scientific community a summary of the current knowledge on animal protein toxins. The aim of this program is to systematically annotate all proteins which act as toxins and are produced by venomous and poisonous animals. Venomous animals such as snakes, scorpions, spiders, jellyfish, insects, cone snails, sea anemones, lizards, some fish, and platypus are equipped with a specialized organ to inject venom in their prey. In contrast, poisonous animals such as some fish or worms, lack such organs. Each toxin is annotated according to the quality standards of Swiss-Prot. This means providing a wealth of information that includes the description of the function, domain structure, subcellular location, tissue specificity, variants, similarities to other proteins, keywords, etc. In the framework of this program, particular care has been made to capture what is known on the function and mode of action, posttranslational modifications and 3D structural data which are all relatively abundant in the field of protein toxins. Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to Swiss-Prot concerning toxins at Tox-Prot@isb-sib.ch. More information on Tox-Prot can be found at http://www.expasy.org/sprot/tox-prot.
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                Author and article information

                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                Nucleic Acids Research
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                January 2007
                7 November 2006
                07 November 2006
                : 35
                : Database issue
                : D391-D394
                Affiliations
                Pathogen Bioinformatics, Mailstop L-174 Energy, Environment, and Biology Division, Computations Directorate, Lawrence Livermore National Laboratory, 70000 East Avenue, Livermore, CA 94550, USA
                1Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
                Author notes
                *To whom correspondence should be addressed. Tel: +1 925 422 2117; Fax: +1 925 423 6437; Email: zhou4@ 123456llnl.gov
                Article
                10.1093/nar/gkl791
                1669772
                17090593
                f2247ea5-46f9-41a8-b112-d09e3d74d6e9
                © 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.

                History
                : 05 June 2006
                : 28 August 2006
                : 02 October 2006
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                Genetics
                Genetics

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