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DPVweb is a database for virologists working on plant viruses combining taxonomic, bioinformatic and symptom data.

Description

DPVweb is a central web-based source of information about viruses, viroids and satellites of plants, fungi and protozoa.^[1]

It provides comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. It makes use of a large database that also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. There are currently about 10,000 such sequences. For comparative purposes, DPVweb also contains a representative sequence of all other fully sequenced virus species with an RNA or single-stranded DNA genome. For each curated sequence the database contains the start and end positions of each feature (gene, non-translated region, etc.), and these have been checked for accuracy. As far as possible, the nomenclature for genes and proteins are standardized within genera and families. Sequences of features (either as DNA or amino acid sequences) can be directly downloaded from the website in FASTA format.^{[citation needed]}

The sequence information can also be accessed via client software for personal computers.

History

The Descriptions of Plant Viruses (DPVs) were first published by the Association of Applied Biologists in 1970 as a series of leaflets, each one written by an expert describing a particular plant virus.^[2] In 1998 all of the 354 DPVs published in paper were scanned, and converted into an electronic format in a database and distributed on CDROM. In 2001 the descriptions were made available on the new DPVweb site, providing open access to the now 400+ DPVs (currently 415) as well as taxonomic and sequence data on all plant viruses.

Uses

DPVweb is an aid to researchers in the field of plant virology as well as an educational resource for students of virology and molecular biology.

The site provides a single point of access for all known plant virus genome sequences making it easy to collect these sequences together for further analysis and comparison. Sequence data from the DPVweb database have proved valuable for a number of projects:

survey of codon usage bias amongst all plant viruses,
two-way comparisons between comprehensive sets of sequences from the families Flexiviridae and Potyviridae that have helped inform taxonomy and clarify genus and species discrimination criteria,
a survey and verification of the polyprotein cleavage sites within the family Potyviridae.

References

^ Adams, M; Antoniw, J (2005). "DPVweb: An open access internet resource on plant viruses and virus diseases". Outlooks on Pest Management. 16 (6): 268–270. doi:10.1564/16dec08.
^ Adams, M; Antoniw, J (January 2006). "DPVweb: a comprehensive database of plant and fungal virus genes and genomes". Nucleic Acids Res. 34 (Database issue): D382–5. doi:10.1093/nar/gkj023. PMC 1347386. PMID 16381892.

Citation by Danish Institute of Agricultural Sciences
Citation by the John Innes Centre, United Kingdom
Adams MJ, Antoniw JF, Fauquet CM (March 2005). "Molecular criteria for genus and species discrimination within the family Potyviridae". Arch. Virol. 150 (3): 459–79. doi:10.1007/s00705-004-0440-6. PMID 15592889. S2CID 20451483.
Adams MJ, Antoniw JF, Beaudoin F (July 2005). "Overview and analysis of the polyprotein cleavage sites in the family Potyviridae". Mol. Plant Pathol. 6 (4): 471–87. doi:10.1111/j.1364-3703.2005.00296.x. PMID 20565672.
Adams MJ, Antoniw JF (January 2004). "Codon usage bias amongst plant viruses". Arch. Virol. 149 (1): 113–35. doi:10.1007/s00705-003-0186-6. PMID 14689279. S2CID 21830222.
Adams MJ, Antoniw JF, Bar-Joseph M, et al. (May 2004). "The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation". Arch. Virol. 149 (5): 1045–60. doi:10.1007/s00705-004-0304-0. PMID 15098118. S2CID 34493607.

External links

Official website
DPVweb EDAM bioinformatics ontology

[researchgate-1] Adams, M; Antoniw, J (2005). "DPVweb: An open access internet resource on plant viruses and virus diseases". Outlooks on Pest Management. 16 (6): 268–270. doi:10.1564/16dec08.

[nist-2] Adams, M; Antoniw, J (January 2006). "DPVweb: a comprehensive database of plant and fungal virus genes and genomes". Nucleic Acids Res. 34 (Database issue): D382–5. doi:10.1093/nar/gkj023. PMC 1347386. PMID 16381892.

[1]

[2]

@@ Line 1: / Line 1: @@
+{{short description|Database for virologists}}
-{{COI|date=June 2007}}
+{{More footnotes needed|date=April 2023}}
-'''DPVweb''' is a [[database]] for virologists working on [[plant viruses]] combining [[taxonomic]], [[bioinformatic]] and [[symptom]] data.
+'''DPVweb''' is a [[database]] for virologists working on [[plant virus]]es combining [[Taxonomy (biology)|taxonomic]], [[bioinformatic]] and [[symptom]] data.
 == Description ==
-DPVweb is a central web-based source of information about [[viruses]], [[viroids]] and satellites of [[plants]], [[fungi]] and [[protozoa]]. It provides comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. It makes use of a large database that also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. There are currently about 10,000 such sequences. For comparative purposes, DPVweb also contains a representative sequence of all other fully sequenced virus species with an [[RNA]] or single-stranded [[DNA]] [[genome]]. For each curated sequence the database contains the start and end positions of each feature ([[gene]], non-translated region, etc), and these have been checked for accuracy. As far as possible, the nomenclature for genes and [[proteins]] are standardized within genera and families. Sequences of features (either as DNA or [[amino acid]] sequences) can be directly downloaded from the website in [[FASTA]] format.
+DPVweb is a central web-based source of information about [[virus]]es, [[viroid]]s and satellites of [[plants]], [[fungi]] and [[protozoa]].<ref name=researchgate>{{cite journal|doi=10.1564/16dec08|last1=Adams|first1=M|last2=Antoniw|first2=J|title=DPVweb: An open access internet resource on plant viruses and virus diseases|journal=Outlooks on Pest Management|volume=16|pages=268–270|year=2005|issue=6 }}</ref>
+It provides comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. It makes use of a large database that also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. There are currently about 10,000 such sequences. For comparative purposes, DPVweb also contains a representative sequence of all other fully sequenced virus species with an [[RNA]] or single-stranded [[DNA]] [[genome]]. For each curated sequence the database contains the start and end positions of each feature ([[gene]], non-translated region, etc.), and these have been checked for accuracy. As far as possible, the nomenclature for genes and [[protein]]s are standardized within genera and families. Sequences of features (either as DNA or [[amino acid]] sequences) can be directly downloaded from the website in [[FASTA]] format.{{citation needed|date=October 2023}}
 The sequence information can also be accessed via client software for personal computers.
 == History ==
-The Descriptions of Plant Viruses (DPVs) were first published by the [[Association of Applied Biologists]] in 1970 as a series of leaflets, each one written by an expert describing a particular plant virus. In 1998 all of the 354 DPVs published in paper were scanned, and converted into an electronic format in a database and distributed on CDROM. In 2001 the descriptions were made available on the new DPVweb site, providing open access to the now 400+ DPVs (currently 415) as well as taxonomic and sequence data on all plant viruses.
+The Descriptions of Plant Viruses (DPVs) were first published by the [[Association of Applied Biologists]] in 1970 as a series of leaflets, each one written by an expert describing a particular plant virus.<ref name=nist>{{cite journal |last1=Adams|first1=M|last2=Antoniw|first2=J|title=DPVweb: a comprehensive database of plant and fungal virus genes and genomes|journal=Nucleic Acids Res.|volume=34|issue=Database issue|pages=D382–5|date=January 2006|pmid=16381892|pmc=1347386 |doi=10.1093/nar/gkj023|url=}}</ref> In 1998 all of the 354 DPVs published in paper were scanned, and converted into an electronic format in a database and distributed on CDROM. In 2001 the descriptions were made available on the new DPVweb site, providing open access to the now 400+ DPVs (currently 415) as well as taxonomic and sequence data on all plant viruses.
-== Uses==
+==Uses==
 DPVweb is an aid to researchers in the field of plant virology as well as an educational resource for students of [[virology]] and [[molecular biology]].
 The site provides a single point of access for all known plant virus genome sequences making it easy to collect these sequences together for further analysis and comparison. Sequence data from the DPVweb database have proved valuable for a number of projects:
 # survey of [[codon]] usage bias amongst all plant viruses,
 # two-way comparisons between comprehensive sets of sequences from the families [[Flexiviridae]] and [[Potyviridae]] that have helped inform taxonomy and clarify genus and species discrimination criteria,
 # a survey and verification of the polyprotein cleavage sites within the family Potyviridae.
 == See also ==
-* [[Plant viruses]]
 * [[Transmission of plant viruses]]
-* [[Caulimoviridae]]
-* [[Geminiviridae]]
-* [[Nanoviridae]]
-* [[Begomovirus]]
-* [[Tombusvirus]]
-* [[Lettuce mosaic virus]]
-* [[Tobacco mosaic virus]]
-==External links==
-* http://www.dpvweb.net
 == References ==
+{{Reflist|30em}}
-*[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=16381892&dopt=Abstract Entry on PubMed]
+{{Refbegin}}
-*[http://www.dias.kvl.dk/plantvirology/seedborne.html Citation by Danish Institute of Agricultural Sciences]
+* [https://web.archive.org/web/20070609202505/http://www.dias.kvl.dk/Plantvirology/seedborne.html Citation by Danish Institute of Agricultural Sciences]
-*[http://www.jic.ac.uk/corporate/search/depart_pub.asp?PUNO=6&offset=100 Citation by the John Innes Centre, United Kingdom]
+* [https://web.archive.org/web/20070930080026/http://www.jic.ac.uk/corporate/search/depart_pub.asp?PUNO=6&offset=100 Citation by the John Innes Centre, United Kingdom]
-*[http://cat.inist.fr/?aModele=afficheN&cpsidt=15468169 Citation by the Centre National del la Recherche Scientifique, France]
+* {{cite journal |vauthors=Adams MJ, Antoniw JF, Fauquet CM |title=Molecular criteria for genus and species discrimination within the family ''Potyviridae'' |journal=Arch. Virol. |volume=150 |issue=3 |pages=459–79 |date=March 2005 |pmid=15592889 |doi=10.1007/s00705-004-0440-6|s2cid=20451483 }}
-* Adams, M.J. & Antoniw, J.F. (2006). DPVweb: a comprehensive database of plant and fungal virus genes and genomes. Nucleic Acids Research 34, Database issue, D382-D385.
+* {{cite journal |vauthors=Adams MJ, Antoniw JF, Beaudoin F |title=Overview and analysis of the polyprotein cleavage sites in the family ''Potyviridae'' |journal=Mol. Plant Pathol. |volume=6 |issue=4 |pages=471–87 |date=July 2005 |pmid=20565672 |doi=10.1111/j.1364-3703.2005.00296.x|doi-access=free }}
-* Adams, M.J. & Antoniw, J.F. (2005). DPVweb: An open access internet resource on plant viruses and virus diseases. Outlooks on Pest Management 16, 268-270.
+* {{cite journal |vauthors=Adams MJ, Antoniw JF |title=Codon usage bias amongst plant viruses |journal=Arch. Virol. |volume=149 |issue=1 |pages=113–35 |date=January 2004 |pmid=14689279 |doi=10.1007/s00705-003-0186-6|s2cid=21830222 }}
-* Adams, M.J., Antoniw, J.F. & Fauquet, C.M. (2005) Molecular criteria for genus and species discrimination within the family Potyviridae. Arch. Virol., 150, 459–479.
+* {{cite journal |vauthors=Adams MJ, Antoniw JF, Bar-Joseph M |title=The new plant virus family ''Flexiviridae'' and assessment of molecular criteria for species demarcation |journal=Arch. Virol. |volume=149 |issue=5 |pages=1045–60 |date=May 2004 |pmid=15098118 |doi=10.1007/s00705-004-0304-0|s2cid=34493607 |display-authors=etal|doi-access=free }}
-* Adams, M.J., Antoniw, J.F. & Beaudoin, F. (2005) Overview and analysis of the polyprotein cleavage sites in the family Potyviridae. Mol. Plant Pathol., 6, 471–487.
+{{Refend}}
-* Adams, M.J. & Antoniw, J.F. (2004) Codon usage bias amongst plant viruses. Arch. Virol., 149, 113–135.
-* Adams, M.J., Antoniw, J.F., Bar-Joseph, M., Brunt, A.A., Candresse, T., Foster, G.D., Martelli, G.P., Milne, R.G., Zavriev, S.K. & Fauquet, C.M. (2004) The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation. Arch. Virol., 149, 1045–1060.
+== External links ==
+* {{Official website|http://www.dpvweb.net}}
+* [http://bioportal.bioontology.org/ontologies/EDAM?p=classes&conceptid=data_2836 DPVweb] ''EDAM bioinformatics ontology''
+{{DEFAULTSORT:Dpvweb}}
-[[Category:Bioinformatics databases]]
 [[Category:Molecular biology]]
 [[Category:Plant taxonomy]]
-[[Category:Plant pathogens and diseases]]
+[[Category:Biological databases]]
+[[Category:Viral plant pathogens and diseases]]
 [[Category:Virology]]
-[[Category:Microbiology]]
+[[Category:Ontology (information science)]]
+[[Category:Information science]]