MRPrimerV: a database of PCR primers for RNA virus detection.
Identifieur interne : 000C30 ( PubMed/Checkpoint ); précédent : 000C29; suivant : 000C31MRPrimerV: a database of PCR primers for RNA virus detection.
Auteurs : Hyerin Kim [Corée du Sud] ; Nana Kang [Corée du Sud] ; Kyuhyeon An [Corée du Sud] ; Doyun Kim [Corée du Sud] ; Jaehyung Koo [Corée du Sud] ; Min-Soo Kim [Corée du Sud]Source :
- Nucleic acids research [ 1362-4962 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
- diagnostic : Maladies virales.
- génétique : Virus à ARN.
- virologie : Maladies virales.
- Amorces ADN, Bases de données d'acides nucléiques, Humains, Réaction de polymérisation en chaîne.
English descriptors
- KwdEn :
- MESH :
- chemical : DNA Primers.
- diagnosis : Virus Diseases.
- genetics : RNA Viruses.
- virology : Virus Diseases.
- Databases, Nucleic Acid, Humans, Polymerase Chain Reaction.
Abstract
Many infectious diseases are caused by viral infections, and in particular by RNA viruses such as MERS, Ebola and Zika. To understand viral disease, detection and identification of these viruses are essential. Although PCR is widely used for rapid virus identification due to its low cost and high sensitivity and specificity, very few online database resources have compiled PCR primers for RNA viruses. To effectively detect viruses, the MRPrimerV database (http://MRPrimerV.com) contains 152 380 247 PCR primer pairs for detection of 1818 viruses, covering 7144 coding sequences (CDSs), representing 100% of the RNA viruses in the most up-to-date NCBI RefSeq database. Due to rigorous similarity testing against all human and viral sequences, every primer in MRPrimerV is highly target-specific. Because MRPrimerV ranks CDSs by the penalty scores of their best primer, users need only use the first primer pair for a single-phase PCR or the first two primer pairs for two-phase PCR. Moreover, MRPrimerV provides the list of genome neighbors that can be detected using each primer pair, covering 22 192 variants of 532 RefSeq RNA viruses. We believe that the public availability of MRPrimerV will facilitate viral metagenomics studies aimed at evaluating the variability of viruses, as well as other scientific tasks.
DOI: 10.1093/nar/gkw1095
PubMed: 27899620
Affiliations:
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Kim</name><affiliation wicri:level="1"><nlm:affiliation>Department of Information and Communication Engineering, DGIST, Daegu, 42988, South Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Department of Information and Communication Engineering, DGIST, Daegu, 42988</wicri:regionArea><wicri:noRegion>42988</wicri:noRegion></affiliation></author><author><name sortKey="Kang, Nana" sort="Kang, Nana" uniqKey="Kang N" first="Nana" last="Kang">Nana Kang</name><affiliation wicri:level="1"><nlm:affiliation>Department of Brain and Cognitive Sciences, DGIST, Daegu, 42988, South Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Department of Brain and Cognitive Sciences, DGIST, Daegu, 42988</wicri:regionArea><wicri:noRegion>42988</wicri:noRegion></affiliation></author><author><name sortKey="An, Kyuhyeon" sort="An, Kyuhyeon" uniqKey="An K" first="Kyuhyeon" last="An">Kyuhyeon An</name><affiliation wicri:level="1"><nlm:affiliation>Department of Information and Communication Engineering, DGIST, Daegu, 42988, South Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Department of Information and Communication Engineering, DGIST, Daegu, 42988</wicri:regionArea><wicri:noRegion>42988</wicri:noRegion></affiliation></author><author><name sortKey="Kim, Doyun" sort="Kim, Doyun" uniqKey="Kim D" first="Doyun" last="Kim">Doyun Kim</name><affiliation wicri:level="1"><nlm:affiliation>Department of Brain and Cognitive Sciences, DGIST, Daegu, 42988, South Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Department of Brain and Cognitive Sciences, DGIST, Daegu, 42988</wicri:regionArea><wicri:noRegion>42988</wicri:noRegion></affiliation></author><author><name sortKey="Koo, Jaehyung" sort="Koo, Jaehyung" uniqKey="Koo J" first="Jaehyung" last="Koo">Jaehyung Koo</name><affiliation wicri:level="1"><nlm:affiliation>Department of Brain and Cognitive Sciences, DGIST, Daegu, 42988, South Korea jkoo001@dgist.ac.kr.</nlm:affiliation><country wicri:rule="url">Corée du Sud</country><wicri:regionArea>Department of Brain and Cognitive Sciences, DGIST, Daegu, 42988</wicri:regionArea><wicri:noRegion>42988</wicri:noRegion></affiliation></author><author><name sortKey="Kim, Min Soo" sort="Kim, Min Soo" uniqKey="Kim M" first="Min-Soo" last="Kim">Min-Soo Kim</name><affiliation wicri:level="1"><nlm:affiliation>Department of Information and Communication Engineering, DGIST, Daegu, 42988, South Korea mskim@dgist.ac.kr.</nlm:affiliation><country wicri:rule="url">Corée du Sud</country><wicri:regionArea>Department of Information and Communication Engineering, DGIST, Daegu, 42988</wicri:regionArea><wicri:noRegion>42988</wicri:noRegion></affiliation></author></analytic><series><title level="j">Nucleic acids research</title><idno type="eISSN">1362-4962</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>DNA Primers</term><term>Databases, Nucleic Acid</term><term>Humans</term><term>Polymerase Chain Reaction</term><term>RNA Viruses (genetics)</term><term>Virus Diseases (diagnosis)</term><term>Virus Diseases (virology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Amorces ADN</term><term>Bases de données d'acides nucléiques</term><term>Humains</term><term>Maladies virales (diagnostic)</term><term>Maladies virales (virologie)</term><term>Réaction de polymérisation en chaîne</term><term>Virus à ARN (génétique)</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>DNA Primers</term></keywords><keywords scheme="MESH" qualifier="diagnosis" xml:lang="en"><term>Virus Diseases</term></keywords><keywords scheme="MESH" qualifier="diagnostic" xml:lang="fr"><term>Maladies virales</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>RNA Viruses</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Virus à ARN</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Maladies virales</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Virus Diseases</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Nucleic Acid</term><term>Humans</term><term>Polymerase Chain Reaction</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Amorces ADN</term><term>Bases de données d'acides nucléiques</term><term>Humains</term><term>Réaction de polymérisation en chaîne</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Many infectious diseases are caused by viral infections, and in particular by RNA viruses such as MERS, Ebola and Zika. To understand viral disease, detection and identification of these viruses are essential. Although PCR is widely used for rapid virus identification due to its low cost and high sensitivity and specificity, very few online database resources have compiled PCR primers for RNA viruses. To effectively detect viruses, the MRPrimerV database (http://MRPrimerV.com) contains 152 380 247 PCR primer pairs for detection of 1818 viruses, covering 7144 coding sequences (CDSs), representing 100% of the RNA viruses in the most up-to-date NCBI RefSeq database. Due to rigorous similarity testing against all human and viral sequences, every primer in MRPrimerV is highly target-specific. Because MRPrimerV ranks CDSs by the penalty scores of their best primer, users need only use the first primer pair for a single-phase PCR or the first two primer pairs for two-phase PCR. Moreover, MRPrimerV provides the list of genome neighbors that can be detected using each primer pair, covering 22 192 variants of 532 RefSeq RNA viruses. We believe that the public availability of MRPrimerV will facilitate viral metagenomics studies aimed at evaluating the variability of viruses, as well as other scientific tasks.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">27899620</PMID><DateCompleted><Year>2017</Year><Month>06</Month><Day>15</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1362-4962</ISSN><JournalIssue CitedMedium="Internet"><Volume>45</Volume><Issue>D1</Issue><PubDate><Year>2017</Year><Month>01</Month><Day>04</Day></PubDate></JournalIssue><Title>Nucleic acids research</Title><ISOAbbreviation>Nucleic Acids Res.</ISOAbbreviation></Journal><ArticleTitle>MRPrimerV: a database of PCR primers for RNA virus detection.</ArticleTitle><Pagination><MedlinePgn>D475-D481</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/nar/gkw1095</ELocationID><Abstract><AbstractText>Many infectious diseases are caused by viral infections, and in particular by RNA viruses such as MERS, Ebola and Zika. To understand viral disease, detection and identification of these viruses are essential. Although PCR is widely used for rapid virus identification due to its low cost and high sensitivity and specificity, very few online database resources have compiled PCR primers for RNA viruses. To effectively detect viruses, the MRPrimerV database (http://MRPrimerV.com) contains 152 380 247 PCR primer pairs for detection of 1818 viruses, covering 7144 coding sequences (CDSs), representing 100% of the RNA viruses in the most up-to-date NCBI RefSeq database. Due to rigorous similarity testing against all human and viral sequences, every primer in MRPrimerV is highly target-specific. Because MRPrimerV ranks CDSs by the penalty scores of their best primer, users need only use the first primer pair for a single-phase PCR or the first two primer pairs for two-phase PCR. Moreover, MRPrimerV provides the list of genome neighbors that can be detected using each primer pair, covering 22 192 variants of 532 RefSeq RNA viruses. We believe that the public availability of MRPrimerV will facilitate viral metagenomics studies aimed at evaluating the variability of viruses, as well as other scientific tasks.</AbstractText><CopyrightInformation>© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Hyerin</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Department of Information and Communication Engineering, DGIST, Daegu, 42988, South Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kang</LastName><ForeName>NaNa</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Department of Brain and Cognitive Sciences, DGIST, Daegu, 42988, South Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>An</LastName><ForeName>KyuHyeon</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Information and Communication Engineering, DGIST, Daegu, 42988, South Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Doyun</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Brain and Cognitive Sciences, DGIST, Daegu, 42988, South Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Koo</LastName><ForeName>JaeHyung</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Brain and Cognitive Sciences, DGIST, Daegu, 42988, South Korea jkoo001@dgist.ac.kr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Min-Soo</ForeName><Initials>MS</Initials><AffiliationInfo><Affiliation>Department of Information and Communication Engineering, DGIST, Daegu, 42988, South Korea mskim@dgist.ac.kr.</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>2016</Year><Month>11</Month><Day>29</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Nucleic Acids Res</MedlineTA><NlmUniqueID>0411011</NlmUniqueID><ISSNLinking>0305-1048</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D017931">DNA Primers</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D017931" MajorTopicYN="Y">DNA Primers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D030561" MajorTopicYN="Y">Databases, Nucleic Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016133" MajorTopicYN="Y">Polymerase Chain Reaction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012328" MajorTopicYN="N">RNA Viruses</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014777" MajorTopicYN="N">Virus Diseases</DescriptorName><QualifierName UI="Q000175" MajorTopicYN="N">diagnosis</QualifierName><QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>10</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2016</Year><Month>10</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>08</Month><Day>15</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>12</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>6</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>12</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27899620</ArticleId><ArticleId IdType="pii">gkw1095</ArticleId><ArticleId IdType="doi">10.1093/nar/gkw1095</ArticleId><ArticleId IdType="pmc">PMC5210568</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Nucleic Acids Res. 2006 Jan 1;34(Database issue):D684-8</Citation><ArticleIdList><ArticleId IdType="pubmed">16381959</ArticleId></ArticleIdList></Reference><Reference><Citation>J Prev Med Public Health. 2015 Nov;48(6):274-6</Citation><ArticleIdList><ArticleId IdType="pubmed">26639740</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2007 Jan;35(Database issue):D805-9</Citation><ArticleIdList><ArticleId IdType="pubmed">17068075</ArticleId></ArticleIdList></Reference><Reference><Citation>N Engl J Med. 2016 Mar 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Jan;42(Database issue):D756-63</Citation><ArticleIdList><ArticleId IdType="pubmed">24259432</ArticleId></ArticleIdList></Reference><Reference><Citation>J Virol. 2004 Jul;78(14):7291-8</Citation><ArticleIdList><ArticleId IdType="pubmed">15220402</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2012 Jan;40(Database issue):D1144-9</Citation><ArticleIdList><ArticleId IdType="pubmed">22086960</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Corée du Sud</li></country></list><tree><country name="Corée du Sud"><noRegion><name sortKey="Kim, Hyerin" sort="Kim, Hyerin" uniqKey="Kim H" first="Hyerin" last="Kim">Hyerin Kim</name></noRegion><name sortKey="An, Kyuhyeon" sort="An, Kyuhyeon" uniqKey="An K" first="Kyuhyeon" last="An">Kyuhyeon An</name><name sortKey="Kang, Nana" sort="Kang, Nana" uniqKey="Kang N" first="Nana" last="Kang">Nana Kang</name><name sortKey="Kim, Doyun" sort="Kim, Doyun" uniqKey="Kim D" first="Doyun" last="Kim">Doyun Kim</name><name sortKey="Kim, Min Soo" sort="Kim, Min Soo" uniqKey="Kim M" first="Min-Soo" last="Kim">Min-Soo Kim</name><name sortKey="Koo, Jaehyung" sort="Koo, Jaehyung" uniqKey="Koo J" first="Jaehyung" last="Koo">Jaehyung Koo</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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