MersV1, PubMed, Corpus, bibRecord, 001F93

Multiplex primer prediction software for divergent targets.

Identifieur interne : 001F93 ( PubMed/Corpus ); précédent : 001F92; suivant : 001F94

Multiplex primer prediction software for divergent targets.

Auteurs : Shea N. Gardner ; Amy L. Hiddessen ; Peter L. Williams ; Christine Hara ; Mark C. Wagner ; Bill W. Colston

Source :

Nucleic acids research [ 1362-4962 ] ; 2009.

RBID : pubmed:19759213

English descriptors

KwdEn :
- Algorithms, DNA (analysis), DNA Primers (chemistry), Humans, RNA Viruses (genetics), Sequence Analysis, DNA, Software, Vaccinia virus (genetics), Viruses (genetics), Viruses (isolation & purification).
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 ( 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.

DOI: 10.1093/nar/gkp659
PubMed: 19759213

Links to Exploration step

pubmed:19759213

Le document en format XML

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<author><name sortKey="Gardner, Shea N" sort="Gardner, Shea N" uniqKey="Gardner S" first="Shea N" last="Gardner">Shea N. Gardner</name>
<affiliation><nlm:affiliation>Computations/Global Security, Lawrence Livermore National Laboratory and QuantaLife, Inc, Livermore, CA, USA. gardner26@llnl.gov</nlm:affiliation>
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<author><name sortKey="Hiddessen, Amy L" sort="Hiddessen, Amy L" uniqKey="Hiddessen A" first="Amy L" last="Hiddessen">Amy L. Hiddessen</name>
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<author><name sortKey="Williams, Peter L" sort="Williams, Peter L" uniqKey="Williams P" first="Peter L" last="Williams">Peter L. Williams</name>
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<author><name sortKey="Hara, Christine" sort="Hara, Christine" uniqKey="Hara C" first="Christine" last="Hara">Christine Hara</name>
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<author><name sortKey="Wagner, Mark C" sort="Wagner, Mark C" uniqKey="Wagner M" first="Mark C" last="Wagner">Mark C. Wagner</name>
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<author><name sortKey="Colston, Bill W" sort="Colston, Bill W" uniqKey="Colston B" first="Bill W" last="Colston">Bill W. Colston</name>
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<author><name sortKey="Gardner, Shea N" sort="Gardner, Shea N" uniqKey="Gardner S" first="Shea N" last="Gardner">Shea N. Gardner</name>
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<author><name sortKey="Hiddessen, Amy L" sort="Hiddessen, Amy L" uniqKey="Hiddessen A" first="Amy L" last="Hiddessen">Amy L. Hiddessen</name>
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<author><name sortKey="Hara, Christine" sort="Hara, Christine" uniqKey="Hara C" first="Christine" last="Hara">Christine Hara</name>
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<author><name sortKey="Wagner, Mark C" sort="Wagner, Mark C" uniqKey="Wagner M" first="Mark C" last="Wagner">Mark C. Wagner</name>
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<author><name sortKey="Colston, Bill W" sort="Colston, Bill W" uniqKey="Colston B" first="Bill W" last="Colston">Bill W. Colston</name>
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<term>DNA (analysis)</term>
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<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>
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<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>
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Multiplex primer prediction software for divergent targets.

Multiplex primer prediction software for divergent targets.

Source :

English descriptors

Abstract

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

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