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|description=A database of toxins, virulence factors and antibiotic resistance genes|scope=Toxins, Virulence Factors and Antibiotic resistance genes|organism=[[Bacteria]]|center=|laboratory=|author=|pmid=17090593|released=|standard=|format=|url={{URL|http://mvirdb.llnl.gov/}}|download=|webservice=|sql=|sparql=|webapp=|standalone=|license=|versioning=|frequency=|curation=|bookmark=yes|version=
|description=A database of toxins, virulence factors and antibiotic resistance genes|scope=Toxins, Virulence Factors and Antibiotic resistance genes|organism=[[Bacteria]]|center=|laboratory=|author=|pmid=17090593|released=|standard=|format=|url={{URL|http://mvirdb.llnl.gov/}}|download=|webservice=|sql=|sparql=|webapp=|standalone=|license=|versioning=|frequency=|curation=|bookmark=yes|version=
}}
}}
'''MvirDB''' is a publicly available [[database]] that stores information on [[toxin]]s, [[virulence factor]]s and [[Antimicrobial resistance|antibiotic resistance]] genes.<ref name=":0">{{Cite journal|last=Zhou|first=C. E.|last2=Smith|first2=J.|last3=Lam|first3=M.|last4=Zemla|first4=A.|last5=Dyer|first5=M. D.|last6=Slezak|first6=T.|date=2007-01-03|title=MvirDB--a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications|url=https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkl791|journal=Nucleic Acids Research|volume=35|issue=Database|pages=D391–D394|doi=10.1093/nar/gkl791|issn=0305-1048}}</ref> Sources that this database uses for [[DNA]] and [[protein]] information include: Tox-Prot,<ref>{{Cite journal|last=Jungo|first=Florence|last2=Bairoch|first2=Amos|date=March 2005|title=Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase|url=http://dx.doi.org/10.1016/j.toxicon.2004.10.018|journal=Toxicon|volume=45|issue=3|pages=293–301|doi=10.1016/j.toxicon.2004.10.018|issn=0041-0101}}</ref> SCORPION,<ref>{{Cite journal|last=Srinivasan|first=K.N.|last2=Gopalakrishnakone|first2=P.|last3=Tan|first3=P.T.|last4=Chew|first4=K.C.|last5=Cheng|first5=B.|last6=Kini|first6=R.M.|last7=Koh|first7=J.L.Y.|last8=Seah|first8=S.H.|last9=Brusic|first9=V.|date=January 2002|title=SCORPION, a molecular database of scorpion toxins|url=http://dx.doi.org/10.1016/s0041-0101(01)00182-9|journal=Toxicon|volume=40|issue=1|pages=23–31|doi=10.1016/s0041-0101(01)00182-9|issn=0041-0101}}</ref> the PRINTS Virulence Factors,<ref>{{Cite journal|date=2008|title=Author Index Vol. 15, No. 1, 2008|url=http://dx.doi.org/10.1159/000121450|journal=Journal of Molecular Microbiology and Biotechnology|volume=15|issue=1|pages=65–65|doi=10.1159/000121450|issn=1464-1801}}</ref><ref>{{Citation|last=Attwood|first=Teresa K.|title=The PRINTS protein fingerprint database: functional and evolutionary applications|date=2005-04-15|url=http://dx.doi.org/10.1002/047001153x.g306301|work=Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics|publisher=John Wiley & Sons, Ltd|isbn=047001153X|access-date=2019-06-27|last2=Bradley|first2=Paul M.|last3=Gaulton|first3=Anna|last4=Maudling|first4=Neil|last5=Mitchell|first5=Alexander L.|last6=Moulton|first6=Georgina}}</ref> [[VFDB]],<ref>{{Cite journal|last=Chen|first=L.|date=2004-12-17|title=VFDB: a reference database for bacterial virulence factors|url=http://dx.doi.org/10.1093/nar/gki008|journal=Nucleic Acids Research|volume=33|issue=Database issue|pages=D325–D328|doi=10.1093/nar/gki008|issn=1362-4962}}</ref> TVFac, Islander,<ref>{{Cite journal|last=Mantri|first=Y.|date=2004-01-01|title=Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities|url=http://dx.doi.org/10.1093/nar/gkh059|journal=Nucleic Acids Research|volume=32|issue=90001|pages=55D–58|doi=10.1093/nar/gkh059|issn=1362-4962}}</ref> ARGO<ref>{{Cite journal|last=Scaria|first=Joy|last2=Chandramouli|first2=Umamaheswaran|last3=Verma|first3=Sanjay Kumar|date=2005-02-01|title=Antibiotic Resistance Genes Online (ARGO): A Database on vancomycin and b-lactam resistance genes|url=http://dx.doi.org/10.6026/97320630001005|journal=Bioinformation|volume=1|issue=1|pages=5–7|doi=10.6026/97320630001005|issn=0973-8894}}</ref> and VIDA.<ref>{{Cite journal|last=Yeats|first=C.|last2=Lees|first2=J.|last3=Reid|first3=A.|last4=Kellam|first4=P.|last5=Martin|first5=N.|last6=Liu|first6=X.|last7=Orengo|first7=C.|date=2007-12-23|title=Gene3D: comprehensive structural and functional annotation of genomes|url=http://dx.doi.org/10.1093/nar/gkm1019|journal=Nucleic Acids Research|volume=36|issue=Database|pages=D414–D418|doi=10.1093/nar/gkm1019|issn=0305-1048}}</ref> The [[database]] provides a [[BLAST]] tool that allows the user to query their sequence against all [[DNA]] and [[protein]] sequences on MvirDB. Information on [[Virulence factor|virulence factors]] can be obtained from the usage of the provided browser tool. Once the browser tool is used, the results are turned as a readable table that is organized by ascending E-Values, each of which are hyperlinked to their related page. MvirDB is implemented on an [[Oracle Database|Oracle 10g]] relational database.<ref name=":0" />
In [[molecular biology]], '''MvirDB''' is a publicly available [[Biological database|database]] that stores information on [[toxin]]s, [[virulence factor]]s and [[Antimicrobial resistance|antibiotic resistance]] genes.<ref name=":0">{{Cite journal|last=Zhou|first=C. E.|last2=Smith|first2=J.|last3=Lam|first3=M.|last4=Zemla|first4=A.|last5=Dyer|first5=M. D.|last6=Slezak|first6=T.|date=2007-01-03|title=MvirDB--a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications|url=https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkl791|journal=Nucleic Acids Research|volume=35|issue=Database|pages=D391–D394|doi=10.1093/nar/gkl791|issn=0305-1048}}</ref> Sources that this database uses for [[DNA]] and [[protein]] information include: Tox-Prot,<ref>{{Cite journal|last=Jungo|first=Florence|last2=Bairoch|first2=Amos|date=March 2005|title=Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase|url=http://dx.doi.org/10.1016/j.toxicon.2004.10.018|journal=Toxicon|volume=45|issue=3|pages=293–301|doi=10.1016/j.toxicon.2004.10.018|issn=0041-0101}}</ref> SCORPION,<ref>{{Cite journal|last=Srinivasan|first=K.N.|last2=Gopalakrishnakone|first2=P.|last3=Tan|first3=P.T.|last4=Chew|first4=K.C.|last5=Cheng|first5=B.|last6=Kini|first6=R.M.|last7=Koh|first7=J.L.Y.|last8=Seah|first8=S.H.|last9=Brusic|first9=V.|date=January 2002|title=SCORPION, a molecular database of scorpion toxins|url=http://dx.doi.org/10.1016/s0041-0101(01)00182-9|journal=Toxicon|volume=40|issue=1|pages=23–31|doi=10.1016/s0041-0101(01)00182-9|issn=0041-0101}}</ref> the PRINTS Virulence Factors,<ref>{{Cite journal|date=2008|title=Author Index Vol. 15, No. 1, 2008|url=http://dx.doi.org/10.1159/000121450|journal=Journal of Molecular Microbiology and Biotechnology|volume=15|issue=1|pages=65–65|doi=10.1159/000121450|issn=1464-1801}}</ref><ref>{{Citation|last=Attwood|first=Teresa K.|title=The PRINTS protein fingerprint database: functional and evolutionary applications|date=2005-04-15|url=http://dx.doi.org/10.1002/047001153x.g306301|work=Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics|publisher=John Wiley & Sons, Ltd|isbn=047001153X|access-date=2019-06-27|last2=Bradley|first2=Paul M.|last3=Gaulton|first3=Anna|last4=Maudling|first4=Neil|last5=Mitchell|first5=Alexander L.|last6=Moulton|first6=Georgina}}</ref> [[VFDB]],<ref>{{Cite journal|last=Chen|first=L.|date=2004-12-17|title=VFDB: a reference database for bacterial virulence factors|url=http://dx.doi.org/10.1093/nar/gki008|journal=Nucleic Acids Research|volume=33|issue=Database issue|pages=D325–D328|doi=10.1093/nar/gki008|issn=1362-4962}}</ref> TVFac, Islander,<ref>{{Cite journal|last=Mantri|first=Y.|date=2004-01-01|title=Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities|url=http://dx.doi.org/10.1093/nar/gkh059|journal=Nucleic Acids Research|volume=32|issue=90001|pages=55D–58|doi=10.1093/nar/gkh059|issn=1362-4962}}</ref> ARGO<ref>{{Cite journal|last=Scaria|first=Joy|last2=Chandramouli|first2=Umamaheswaran|last3=Verma|first3=Sanjay Kumar|date=2005-02-01|title=Antibiotic Resistance Genes Online (ARGO): A Database on vancomycin and b-lactam resistance genes|url=http://dx.doi.org/10.6026/97320630001005|journal=Bioinformation|volume=1|issue=1|pages=5–7|doi=10.6026/97320630001005|issn=0973-8894}}</ref> and VIDA.<ref>{{Cite journal|last=Yeats|first=C.|last2=Lees|first2=J.|last3=Reid|first3=A.|last4=Kellam|first4=P.|last5=Martin|first5=N.|last6=Liu|first6=X.|last7=Orengo|first7=C.|date=2007-12-23|title=Gene3D: comprehensive structural and functional annotation of genomes|url=http://dx.doi.org/10.1093/nar/gkm1019|journal=Nucleic Acids Research|volume=36|issue=Database|pages=D414–D418|doi=10.1093/nar/gkm1019|issn=0305-1048}}</ref> The database provides a [[BLAST]] tool that allows the user to query their sequence against all [[DNA]] and [[protein]] sequences in MvirDB. Information on [[Virulence factor|virulence factors]] can be obtained from the usage of the provided browser tool. Once the browser tool is used, the results are returned as a readable table that is organized by ascending E-Values, each of which are hyperlinked to their related page. MvirDB is implemented in an [[Oracle Database|Oracle 10g]] relational database.<ref name=":0" />


== See also ==
== See also ==

Revision as of 20:20, 9 July 2019

MvirDB
Content
DescriptionA database of toxins, virulence factors and antibiotic resistance genes
Data types
captured		Toxins, Virulence Factors and Antibiotic resistance genes
OrganismsBacteria
Contact
Primary citationPMID 17090593
Access
Websitemvirdb.llnl.gov
Miscellaneous
Bookmarkable
entities		yes

In molecular biology, MvirDB is a publicly available database that stores information on toxins, virulence factors and antibiotic resistance genes.[1] Sources that this database uses for DNA and protein information include: Tox-Prot,[2] SCORPION,[3] the PRINTS Virulence Factors,[4][5] VFDB,[6] TVFac, Islander,[7] ARGO[8] and VIDA.[9] The database provides a BLAST tool that allows the user to query their sequence against all DNA and protein sequences in MvirDB. Information on virulence factors can be obtained from the usage of the provided browser tool. Once the browser tool is used, the results are returned as a readable table that is organized by ascending E-Values, each of which are hyperlinked to their related page. MvirDB is implemented in an Oracle 10g relational database.[1]

See also

References

  1. ^ a b Zhou, C. E.; Smith, J.; Lam, M.; Zemla, A.; Dyer, M. D.; Slezak, T. (2007-01-03). "MvirDB--a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications". Nucleic Acids Research. 35 (Database): D391–D394. doi:10.1093/nar/gkl791. ISSN 0305-1048.
  2. ^ Jungo, Florence; Bairoch, Amos (March 2005). "Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase". Toxicon. 45 (3): 293–301. doi:10.1016/j.toxicon.2004.10.018. ISSN 0041-0101.
  3. ^ Srinivasan, K.N.; Gopalakrishnakone, P.; Tan, P.T.; Chew, K.C.; Cheng, B.; Kini, R.M.; Koh, J.L.Y.; Seah, S.H.; Brusic, V. (January 2002). "SCORPION, a molecular database of scorpion toxins". Toxicon. 40 (1): 23–31. doi:10.1016/s0041-0101(01)00182-9. ISSN 0041-0101.
  4. ^ "Author Index Vol. 15, No. 1, 2008". Journal of Molecular Microbiology and Biotechnology. 15 (1): 65–65. 2008. doi:10.1159/000121450. ISSN 1464-1801.
  5. ^ Attwood, Teresa K.; Bradley, Paul M.; Gaulton, Anna; Maudling, Neil; Mitchell, Alexander L.; Moulton, Georgina (2005-04-15), "The PRINTS protein fingerprint database: functional and evolutionary applications", Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, John Wiley & Sons, Ltd, ISBN 047001153X, retrieved 2019-06-27
  6. ^ Chen, L. (2004-12-17). "VFDB: a reference database for bacterial virulence factors". Nucleic Acids Research. 33 (Database issue): D325–D328. doi:10.1093/nar/gki008. ISSN 1362-4962.
  7. ^ Mantri, Y. (2004-01-01). "Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities". Nucleic Acids Research. 32 (90001): 55D–58. doi:10.1093/nar/gkh059. ISSN 1362-4962.
  8. ^ Scaria, Joy; Chandramouli, Umamaheswaran; Verma, Sanjay Kumar (2005-02-01). "Antibiotic Resistance Genes Online (ARGO): A Database on vancomycin and b-lactam resistance genes". Bioinformation. 1 (1): 5–7. doi:10.6026/97320630001005. ISSN 0973-8894.
  9. ^ Yeats, C.; Lees, J.; Reid, A.; Kellam, P.; Martin, N.; Liu, X.; Orengo, C. (2007-12-23). "Gene3D: comprehensive structural and functional annotation of genomes". Nucleic Acids Research. 36 (Database): D414–D418. doi:10.1093/nar/gkm1019. ISSN 0305-1048.
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