WNV Typer: a server for genotyping of West Nile viruses using an alignment-free method based on a return time distribution.
Identifieur interne : 001A96 ( PubMed/Corpus ); précédent : 001A95; suivant : 001A97WNV Typer: a server for genotyping of West Nile viruses using an alignment-free method based on a return time distribution.
Auteurs : Pandurang Kolekar ; Nilesh Hake ; Mohan Kale ; Urmila Kulkarni-KaleSource :
- Journal of virological methods [ 1879-0984 ] ; 2014.
English descriptors
- KwdEn :
- MESH :
- genetics : Genome, Viral, West Nile virus.
- methods : Sequence Analysis.
- virology : West Nile Fever.
- Genotype, Phylogeny.
Abstract
West Nile virus (WNV), genus Flavivirus, family Flaviviridae, is a major cause of viral encephalitis with broad host range and global spread. The virus has undergone a series of evolutionary changes with emergence of various genotypic lineages that are known to differ in type and severity of the diseases caused. Currently, genotyping is carried out using molecular phylogeny of complete coding sequences and genotype is assigned based on proximity to reference genotypes in tree topology. Efficient epidemiological surveillance of WNVs demands development of objective criteria for typing. An alignment-free approach based on return time distribution (RTD) of k-mers has been validated for genotyping of WNVs. The RTDs of complete genome sequences at k=7 were found to be optimum for classification of the known lineages of WNVs as well as for genotyping. It provides time and computationally efficient alternative for genome based annotation of WNV lineages. The development of a WNV Typer server based on RTD is described (http://bioinfo.net.in/wnv/homepage.html). Both the method and the server have 100% sensitivity and specificity.
DOI: 10.1016/j.jviromet.2013.12.012
PubMed: 24388930
Links to Exploration step
pubmed:24388930Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">WNV Typer: a server for genotyping of West Nile viruses using an alignment-free method based on a return time distribution.</title><author><name sortKey="Kolekar, Pandurang" sort="Kolekar, Pandurang" uniqKey="Kolekar P" first="Pandurang" last="Kolekar">Pandurang Kolekar</name><affiliation><nlm:affiliation>Bioinformatics Centre, University of Pune, Pune 411007, India. Electronic address: pandurang@bioinfo.net.in.</nlm:affiliation></affiliation></author><author><name sortKey="Hake, Nilesh" sort="Hake, Nilesh" uniqKey="Hake N" first="Nilesh" last="Hake">Nilesh Hake</name><affiliation><nlm:affiliation>Bioinformatics Centre, University of Pune, Pune 411007, India.</nlm:affiliation></affiliation></author><author><name sortKey="Kale, Mohan" sort="Kale, Mohan" uniqKey="Kale M" first="Mohan" last="Kale">Mohan Kale</name><affiliation><nlm:affiliation>Department of Statistics, University of Pune, Pune 411007, India. Electronic address: mmkale@stats.unipune.ac.in.</nlm:affiliation></affiliation></author><author><name sortKey="Kulkarni Kale, Urmila" sort="Kulkarni Kale, Urmila" uniqKey="Kulkarni Kale U" first="Urmila" last="Kulkarni-Kale">Urmila Kulkarni-Kale</name><affiliation><nlm:affiliation>Bioinformatics Centre, University of Pune, Pune 411007, India. Electronic address: urmila@bioinfo.net.in.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:24388930</idno><idno type="pmid">24388930</idno><idno type="doi">10.1016/j.jviromet.2013.12.012</idno><idno type="wicri:Area/PubMed/Corpus">001A96</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001A96</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">WNV Typer: a server for genotyping of West Nile viruses using an alignment-free method based on a return time distribution.</title><author><name sortKey="Kolekar, Pandurang" sort="Kolekar, Pandurang" uniqKey="Kolekar P" first="Pandurang" last="Kolekar">Pandurang Kolekar</name><affiliation><nlm:affiliation>Bioinformatics Centre, University of Pune, Pune 411007, India. Electronic address: pandurang@bioinfo.net.in.</nlm:affiliation></affiliation></author><author><name sortKey="Hake, Nilesh" sort="Hake, Nilesh" uniqKey="Hake N" first="Nilesh" last="Hake">Nilesh Hake</name><affiliation><nlm:affiliation>Bioinformatics Centre, University of Pune, Pune 411007, India.</nlm:affiliation></affiliation></author><author><name sortKey="Kale, Mohan" sort="Kale, Mohan" uniqKey="Kale M" first="Mohan" last="Kale">Mohan Kale</name><affiliation><nlm:affiliation>Department of Statistics, University of Pune, Pune 411007, India. Electronic address: mmkale@stats.unipune.ac.in.</nlm:affiliation></affiliation></author><author><name sortKey="Kulkarni Kale, Urmila" sort="Kulkarni Kale, Urmila" uniqKey="Kulkarni Kale U" first="Urmila" last="Kulkarni-Kale">Urmila Kulkarni-Kale</name><affiliation><nlm:affiliation>Bioinformatics Centre, University of Pune, Pune 411007, India. Electronic address: urmila@bioinfo.net.in.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Journal of virological methods</title><idno type="eISSN">1879-0984</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Genome, Viral (genetics)</term><term>Genotype</term><term>Phylogeny</term><term>Sequence Analysis (methods)</term><term>West Nile Fever (virology)</term><term>West Nile virus (genetics)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genome, Viral</term><term>West Nile virus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>West Nile Fever</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genotype</term><term>Phylogeny</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">West Nile virus (WNV), genus Flavivirus, family Flaviviridae, is a major cause of viral encephalitis with broad host range and global spread. The virus has undergone a series of evolutionary changes with emergence of various genotypic lineages that are known to differ in type and severity of the diseases caused. Currently, genotyping is carried out using molecular phylogeny of complete coding sequences and genotype is assigned based on proximity to reference genotypes in tree topology. Efficient epidemiological surveillance of WNVs demands development of objective criteria for typing. An alignment-free approach based on return time distribution (RTD) of k-mers has been validated for genotyping of WNVs. The RTDs of complete genome sequences at k=7 were found to be optimum for classification of the known lineages of WNVs as well as for genotyping. It provides time and computationally efficient alternative for genome based annotation of WNV lineages. The development of a WNV Typer server based on RTD is described (http://bioinfo.net.in/wnv/homepage.html). Both the method and the server have 100% sensitivity and specificity. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24388930</PMID><DateCompleted><Year>2014</Year><Month>10</Month><Day>06</Day></DateCompleted><DateRevised><Year>2014</Year><Month>02</Month><Day>14</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1879-0984</ISSN><JournalIssue CitedMedium="Internet"><Volume>198</Volume><PubDate><Year>2014</Year><Month>Mar</Month></PubDate></JournalIssue><Title>Journal of virological methods</Title><ISOAbbreviation>J. Virol. Methods</ISOAbbreviation></Journal><ArticleTitle>WNV Typer: a server for genotyping of West Nile viruses using an alignment-free method based on a return time distribution.</ArticleTitle><Pagination><MedlinePgn>41-55</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.jviromet.2013.12.012</ELocationID><ELocationID EIdType="pii" ValidYN="Y">S0166-0934(13)00514-4</ELocationID><Abstract><AbstractText>West Nile virus (WNV), genus Flavivirus, family Flaviviridae, is a major cause of viral encephalitis with broad host range and global spread. The virus has undergone a series of evolutionary changes with emergence of various genotypic lineages that are known to differ in type and severity of the diseases caused. Currently, genotyping is carried out using molecular phylogeny of complete coding sequences and genotype is assigned based on proximity to reference genotypes in tree topology. Efficient epidemiological surveillance of WNVs demands development of objective criteria for typing. An alignment-free approach based on return time distribution (RTD) of k-mers has been validated for genotyping of WNVs. The RTDs of complete genome sequences at k=7 were found to be optimum for classification of the known lineages of WNVs as well as for genotyping. It provides time and computationally efficient alternative for genome based annotation of WNV lineages. The development of a WNV Typer server based on RTD is described (http://bioinfo.net.in/wnv/homepage.html). Both the method and the server have 100% sensitivity and specificity. </AbstractText><CopyrightInformation>Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kolekar</LastName><ForeName>Pandurang</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Bioinformatics Centre, University of Pune, Pune 411007, India. Electronic address: pandurang@bioinfo.net.in.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hake</LastName><ForeName>Nilesh</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Bioinformatics Centre, University of Pune, Pune 411007, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kale</LastName><ForeName>Mohan</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Statistics, University of Pune, Pune 411007, India. Electronic address: mmkale@stats.unipune.ac.in.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kulkarni-Kale</LastName><ForeName>Urmila</ForeName><Initials>U</Initials><AffiliationInfo><Affiliation>Bioinformatics Centre, University of Pune, Pune 411007, India. Electronic address: urmila@bioinfo.net.in.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>12</Month><Day>31</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>J Virol Methods</MedlineTA><NlmUniqueID>8005839</NlmUniqueID><ISSNLinking>0166-0934</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="N">Genome, Viral</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017421" MajorTopicYN="N">Sequence Analysis</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014901" MajorTopicYN="N">West Nile Fever</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014902" MajorTopicYN="N">West Nile virus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Alignment-free</Keyword><Keyword MajorTopicYN="N">Bioinformatics</Keyword><Keyword MajorTopicYN="N">Genotyping</Keyword><Keyword MajorTopicYN="N">Phylogeny</Keyword><Keyword MajorTopicYN="N">Return time distribution</Keyword><Keyword MajorTopicYN="N">West Nile virus</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2013</Year><Month>07</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2013</Year><Month>11</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2013</Year><Month>12</Month><Day>17</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>1</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>1</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>10</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">24388930</ArticleId><ArticleId IdType="pii">S0166-0934(13)00514-4</ArticleId><ArticleId IdType="doi">10.1016/j.jviromet.2013.12.012</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001A96 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd -nk 001A96 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= PubMed
|étape= Corpus
|type= RBID
|clé= pubmed:24388930
|texte= WNV Typer: a server for genotyping of West Nile viruses using an alignment-free method based on a return time distribution.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/RBID.i -Sk "pubmed:24388930" \
| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |