Multiplex primer prediction software for divergent targets
Identifieur interne : 000712 ( Ncbi/Merge ); précédent : 000711; suivant : 000713Multiplex primer prediction software for divergent targets
Auteurs : Shea N. Gardner ; Amy L. Hiddessen ; Peter L. Williams ; Christine Hara ; Mark C. Wagner ; Bill W. ColstonSource :
- Nucleic Acids Research [ 0305-1048 ] ; 2009.
Descripteurs français
- KwdFr :
- MESH :
- analyse : ADN.
- génétique : Virus, Virus de la vaccine, Virus à ARN.
- isolement et purification : Virus.
- Algorithmes, Amorces ADN, Analyse de séquence d'ADN, Humains, Logiciel.
English descriptors
- KwdEn :
- MESH :
- chemical , analysis : DNA.
- chemical , chemistry : DNA Primers.
- genetics : RNA Viruses, Vaccinia virus, Viruses.
- isolation & purification : Viruses.
- Algorithms, Humans, Sequence Analysis, DNA, Software.
Abstract
We describe a Multiplex Primer Prediction (MPP) algorithm to build multiplex compatible primer sets to amplify all members of large, diverse and unalignable sets of target sequences. The MPP algorithm is scalable to larger target sets than other available software, and it does not require a multiple sequence alignment. We applied it to questions in viral detection, and demonstrated that there are no universally conserved priming sequences among viruses and that it could require an unfeasibly large number of primers (∼3700 18-mers or ∼2000 10-mers) to generate amplicons from all sequenced viruses. We then designed primer sets separately for each viral family, and for several diverse species such as foot-and-mouth disease virus (FMDV), hemagglutinin (HA) and neuraminidase (NA) segments of influenza A virus, Norwalk virus, and HIV-1. We empirically demonstrated the application of the software with a multiplex set of 16 short (10 nt) primers designed to amplify the Poxviridae family to produce a specific amplicon from vaccinia virus.
Url:
DOI: 10.1093/nar/gkp659
PubMed: 19759213
PubMed Central: 2770652
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PMC:2770652Le document en format XML
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Williams</name><affiliation><nlm:aff id="AFF1"></nlm:aff></affiliation></author><author><name sortKey="Hara, Christine" sort="Hara, Christine" uniqKey="Hara C" first="Christine" last="Hara">Christine Hara</name><affiliation><nlm:aff id="AFF1"></nlm:aff></affiliation></author><author><name sortKey="Wagner, Mark C" sort="Wagner, Mark C" uniqKey="Wagner M" first="Mark C." last="Wagner">Mark C. Wagner</name><affiliation><nlm:aff id="AFF1"></nlm:aff></affiliation></author><author><name sortKey="Colston, Bill W" sort="Colston, Bill W" uniqKey="Colston B" first="Bill W." last="Colston">Bill W. 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Gardner</name><affiliation><nlm:aff id="AFF1"></nlm:aff></affiliation></author><author><name sortKey="Hiddessen, Amy L" sort="Hiddessen, Amy L" uniqKey="Hiddessen A" first="Amy L." last="Hiddessen">Amy L. Hiddessen</name><affiliation><nlm:aff id="AFF1"></nlm:aff></affiliation></author><author><name sortKey="Williams, Peter L" sort="Williams, Peter L" uniqKey="Williams P" first="Peter L." last="Williams">Peter L. Williams</name><affiliation><nlm:aff id="AFF1"></nlm:aff></affiliation></author><author><name sortKey="Hara, Christine" sort="Hara, Christine" uniqKey="Hara C" first="Christine" last="Hara">Christine Hara</name><affiliation><nlm:aff id="AFF1"></nlm:aff></affiliation></author><author><name sortKey="Wagner, Mark C" sort="Wagner, Mark C" uniqKey="Wagner M" first="Mark C." last="Wagner">Mark C. Wagner</name><affiliation><nlm:aff id="AFF1"></nlm:aff></affiliation></author><author><name sortKey="Colston, Bill W" sort="Colston, Bill W" uniqKey="Colston B" first="Bill W." last="Colston">Bill W. Colston</name><affiliation><nlm:aff id="AFF1"></nlm:aff></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2009">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>DNA (analysis)</term><term>DNA Primers (chemistry)</term><term>Humans</term><term>RNA Viruses (genetics)</term><term>Sequence Analysis, DNA</term><term>Software</term><term>Vaccinia virus (genetics)</term><term>Viruses (genetics)</term><term>Viruses (isolation & purification)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN (analyse)</term><term>Algorithmes</term><term>Amorces ADN ()</term><term>Analyse de séquence d'ADN</term><term>Humains</term><term>Logiciel</term><term>Virus (génétique)</term><term>Virus (isolement et purification)</term><term>Virus de la vaccine (génétique)</term><term>Virus à ARN (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>DNA</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA Primers</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>ADN</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>RNA Viruses</term><term>Vaccinia virus</term><term>Viruses</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Virus</term><term>Virus de la vaccine</term><term>Virus à ARN</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Viruses</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Virus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Humans</term><term>Sequence Analysis, DNA</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Amorces ADN</term><term>Analyse de séquence d'ADN</term><term>Humains</term><term>Logiciel</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Abstract</title><p>We describe a Multiplex Primer Prediction (MPP) algorithm to build multiplex compatible primer sets to amplify all members of large, diverse and unalignable sets of target sequences. The MPP algorithm is scalable to larger target sets than other available software, and it does not require a multiple sequence alignment. We applied it to questions in viral detection, and demonstrated that there are no universally conserved priming sequences among viruses and that it could require an unfeasibly large number of primers (∼3700 18-mers or ∼2000 10-mers) to generate amplicons from all sequenced viruses. We then designed primer sets separately for each viral family, and for several diverse species such as foot-and-mouth disease virus (FMDV), hemagglutinin (HA) and neuraminidase (NA) segments of influenza A virus, Norwalk virus, and HIV-1. We empirically demonstrated the application of the software with a multiplex set of 16 short (10 nt) primers designed to amplify the Poxviridae family to produce a specific amplicon from vaccinia virus.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Victoria, Jg" uniqKey="Victoria J">JG Victoria</name></author><author><name sortKey="Kapoor, A" uniqKey="Kapoor A">A Kapoor</name></author><author><name sortKey="Li, L" uniqKey="Li L">L Li</name></author><author><name sortKey="Blinkova, O" uniqKey="Blinkova O">O Blinkova</name></author><author><name sortKey="Slikas, B" uniqKey="Slikas B">B Slikas</name></author><author><name sortKey="Wang, C" uniqKey="Wang C">C Wang</name></author><author><name sortKey="Naeem, A" uniqKey="Naeem A">A Naeem</name></author><author><name sortKey="Zaidi, S" uniqKey="Zaidi S">S Zaidi</name></author><author><name sortKey="Delwart, E" uniqKey="Delwart E">E 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Hoek, L" uniqKey="Van Der Hoek L">L van der Hoek</name></author></analytic></biblStruct></listBibl></div1></back></TEI><double pmid="19759213"><pmc><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Multiplex primer prediction software for divergent targets</title><author><name sortKey="Gardner, Shea N" sort="Gardner, Shea N" uniqKey="Gardner S" first="Shea N." last="Gardner">Shea N. Gardner</name><affiliation><nlm:aff id="AFF1"></nlm:aff></affiliation></author><author><name sortKey="Hiddessen, Amy L" sort="Hiddessen, Amy L" uniqKey="Hiddessen A" first="Amy L." last="Hiddessen">Amy L. Hiddessen</name><affiliation><nlm:aff id="AFF1"></nlm:aff></affiliation></author><author><name sortKey="Williams, Peter L" sort="Williams, Peter L" uniqKey="Williams P" first="Peter L." last="Williams">Peter L. Williams</name><affiliation><nlm:aff id="AFF1"></nlm:aff></affiliation></author><author><name sortKey="Hara, Christine" sort="Hara, Christine" uniqKey="Hara C" first="Christine" last="Hara">Christine Hara</name><affiliation><nlm:aff id="AFF1"></nlm:aff></affiliation></author><author><name sortKey="Wagner, Mark C" sort="Wagner, Mark C" uniqKey="Wagner M" first="Mark C." last="Wagner">Mark C. Wagner</name><affiliation><nlm:aff id="AFF1"></nlm:aff></affiliation></author><author><name sortKey="Colston, Bill W" sort="Colston, Bill W" uniqKey="Colston B" first="Bill W." last="Colston">Bill W. Colston</name><affiliation><nlm:aff id="AFF1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">19759213</idno><idno type="pmc">2770652</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770652</idno><idno type="RBID">PMC:2770652</idno><idno type="doi">10.1093/nar/gkp659</idno><date when="2009">2009</date><idno type="wicri:Area/Pmc/Corpus">000F45</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000F45</idno><idno type="wicri:Area/Pmc/Curation">000F45</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000F45</idno><idno type="wicri:Area/Pmc/Checkpoint">001374</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001374</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Multiplex primer prediction software for divergent targets</title><author><name sortKey="Gardner, Shea N" sort="Gardner, Shea N" uniqKey="Gardner S" first="Shea N." last="Gardner">Shea N. Gardner</name><affiliation><nlm:aff id="AFF1"></nlm:aff></affiliation></author><author><name sortKey="Hiddessen, Amy L" sort="Hiddessen, Amy L" uniqKey="Hiddessen A" first="Amy L." last="Hiddessen">Amy L. Hiddessen</name><affiliation><nlm:aff id="AFF1"></nlm:aff></affiliation></author><author><name sortKey="Williams, Peter L" sort="Williams, Peter L" uniqKey="Williams P" first="Peter L." last="Williams">Peter L. Williams</name><affiliation><nlm:aff id="AFF1"></nlm:aff></affiliation></author><author><name sortKey="Hara, Christine" sort="Hara, Christine" uniqKey="Hara C" first="Christine" last="Hara">Christine Hara</name><affiliation><nlm:aff id="AFF1"></nlm:aff></affiliation></author><author><name sortKey="Wagner, Mark C" sort="Wagner, Mark C" uniqKey="Wagner M" first="Mark C." last="Wagner">Mark C. Wagner</name><affiliation><nlm:aff id="AFF1"></nlm:aff></affiliation></author><author><name sortKey="Colston, Bill W" sort="Colston, Bill W" uniqKey="Colston B" first="Bill W." last="Colston">Bill W. Colston</name><affiliation><nlm:aff id="AFF1"></nlm:aff></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2009">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Abstract</title><p>We describe a Multiplex Primer Prediction (MPP) algorithm to build multiplex compatible primer sets to amplify all members of large, diverse and unalignable sets of target sequences. The MPP algorithm is scalable to larger target sets than other available software, and it does not require a multiple sequence alignment. We applied it to questions in viral detection, and demonstrated that there are no universally conserved priming sequences among viruses and that it could require an unfeasibly large number of primers (∼3700 18-mers or ∼2000 10-mers) to generate amplicons from all sequenced viruses. We then designed primer sets separately for each viral family, and for several diverse species such as foot-and-mouth disease virus (FMDV), hemagglutinin (HA) and neuraminidase (NA) segments of influenza A virus, Norwalk virus, and HIV-1. We empirically demonstrated the application of the software with a multiplex set of 16 short (10 nt) primers designed to amplify the Poxviridae family to produce a specific amplicon from vaccinia virus.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Victoria, Jg" uniqKey="Victoria J">JG Victoria</name></author><author><name sortKey="Kapoor, A" uniqKey="Kapoor A">A Kapoor</name></author><author><name sortKey="Li, L" uniqKey="Li L">L Li</name></author><author><name sortKey="Blinkova, O" uniqKey="Blinkova O">O Blinkova</name></author><author><name sortKey="Slikas, B" uniqKey="Slikas B">B Slikas</name></author><author><name sortKey="Wang, C" uniqKey="Wang C">C Wang</name></author><author><name sortKey="Naeem, A" uniqKey="Naeem A">A Naeem</name></author><author><name sortKey="Zaidi, S" uniqKey="Zaidi S">S Zaidi</name></author><author><name sortKey="Delwart, E" uniqKey="Delwart E">E 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Gardner</name><affiliation wicri:level="2"><nlm:affiliation>Computations/Global Security, Lawrence Livermore National Laboratory and QuantaLife, Inc, Livermore, CA, USA. gardner26@llnl.gov</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computations/Global Security, Lawrence Livermore National Laboratory and QuantaLife, Inc, Livermore, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Hiddessen, Amy L" sort="Hiddessen, Amy L" uniqKey="Hiddessen A" first="Amy L" last="Hiddessen">Amy L. Hiddessen</name></author><author><name sortKey="Williams, Peter L" sort="Williams, Peter L" uniqKey="Williams P" first="Peter L" last="Williams">Peter L. Williams</name></author><author><name sortKey="Hara, Christine" sort="Hara, Christine" uniqKey="Hara C" first="Christine" last="Hara">Christine Hara</name></author><author><name sortKey="Wagner, Mark C" sort="Wagner, Mark C" uniqKey="Wagner M" first="Mark C" last="Wagner">Mark C. Wagner</name></author><author><name sortKey="Colston, Bill W" sort="Colston, Bill W" uniqKey="Colston B" first="Bill W" last="Colston">Bill W. Colston</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2009">2009</date><idno type="RBID">pubmed:19759213</idno><idno type="pmid">19759213</idno><idno type="doi">10.1093/nar/gkp659</idno><idno type="wicri:Area/PubMed/Corpus">001F93</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001F93</idno><idno type="wicri:Area/PubMed/Curation">001F93</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001F93</idno><idno type="wicri:Area/PubMed/Checkpoint">001E98</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001E98</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Multiplex primer prediction software for divergent targets.</title><author><name sortKey="Gardner, Shea N" sort="Gardner, Shea N" uniqKey="Gardner S" first="Shea N" last="Gardner">Shea N. Gardner</name><affiliation wicri:level="2"><nlm:affiliation>Computations/Global Security, Lawrence Livermore National Laboratory and QuantaLife, Inc, Livermore, CA, USA. gardner26@llnl.gov</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computations/Global Security, Lawrence Livermore National Laboratory and QuantaLife, Inc, Livermore, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Hiddessen, Amy L" sort="Hiddessen, Amy L" uniqKey="Hiddessen A" first="Amy L" last="Hiddessen">Amy L. Hiddessen</name></author><author><name sortKey="Williams, Peter L" sort="Williams, Peter L" uniqKey="Williams P" first="Peter L" last="Williams">Peter L. Williams</name></author><author><name sortKey="Hara, Christine" sort="Hara, Christine" uniqKey="Hara C" first="Christine" last="Hara">Christine Hara</name></author><author><name sortKey="Wagner, Mark C" sort="Wagner, Mark C" uniqKey="Wagner M" first="Mark C" last="Wagner">Mark C. Wagner</name></author><author><name sortKey="Colston, Bill W" sort="Colston, Bill W" uniqKey="Colston B" first="Bill W" last="Colston">Bill W. Colston</name></author></analytic><series><title level="j">Nucleic acids research</title><idno type="eISSN">1362-4962</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>DNA (analysis)</term><term>DNA Primers (chemistry)</term><term>Humans</term><term>RNA Viruses (genetics)</term><term>Sequence Analysis, DNA</term><term>Software</term><term>Vaccinia virus (genetics)</term><term>Viruses (genetics)</term><term>Viruses (isolation & purification)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN (analyse)</term><term>Algorithmes</term><term>Amorces ADN ()</term><term>Analyse de séquence d'ADN</term><term>Humains</term><term>Logiciel</term><term>Virus (génétique)</term><term>Virus (isolement et purification)</term><term>Virus de la vaccine (génétique)</term><term>Virus à ARN (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>DNA</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA Primers</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>ADN</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>RNA Viruses</term><term>Vaccinia virus</term><term>Viruses</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Virus</term><term>Virus de la vaccine</term><term>Virus à ARN</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Viruses</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Virus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Humans</term><term>Sequence Analysis, DNA</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Amorces ADN</term><term>Analyse de séquence d'ADN</term><term>Humains</term><term>Logiciel</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We describe a Multiplex Primer Prediction (MPP) algorithm to build multiplex compatible primer sets to amplify all members of large, diverse and unalignable sets of target sequences. The MPP algorithm is scalable to larger target sets than other available software, and it does not require a multiple sequence alignment. We applied it to questions in viral detection, and demonstrated that there are no universally conserved priming sequences among viruses and that it could require an unfeasibly large number of primers ( approximately 3700 18-mers or approximately 2000 10-mers) to generate amplicons from all sequenced viruses. We then designed primer sets separately for each viral family, and for several diverse species such as foot-and-mouth disease virus (FMDV), hemagglutinin (HA) and neuraminidase (NA) segments of influenza A virus, Norwalk virus, and HIV-1. We empirically demonstrated the application of the software with a multiplex set of 16 short (10 nt) primers designed to amplify the Poxviridae family to produce a specific amplicon from vaccinia virus.</div></front></TEI></pubmed></double></record>Pour manipuler ce document sous Unix (Dilib)
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