Efficient identification of DNA hybridization partners in a sequence database.
Identifieur interne : 002D31 ( Main/Curation ); précédent : 002D30; suivant : 002D32Efficient identification of DNA hybridization partners in a sequence database.
Auteurs : Tobias P. Mann [États-Unis] ; William Stafford NobleSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2006.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA, DNA Primers.
- genetics : Base Pairing.
- methods : In Situ Hybridization, Sequence Alignment, Sequence Analysis, DNA.
- Algorithms, Base Sequence, Binding Sites, Databases, Genetic, Molecular Sequence Data.
Abstract
The specific hybridization of complementary DNA molecules underlies many widely used molecular biology assays, including the polymerase chain reaction and various types of microarray analysis. In order for such an assay to work well, the primer or probe must bind to its intended target, without also binding to additional sequences in the reaction mixture. For any given probe or primer, potential non-specific binding partners can be identified using state-of-the-art models of DNA binding stability. Unfortunately, these models rely on dynamic programming algorithms that are too slow to apply on a genomic scale.
DOI: 10.1093/bioinformatics/btl240
PubMed: 16873493
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pubmed:16873493Le document en format XML
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<affiliation wicri:level="4"><nlm:affiliation>Department of Genome Sciences, University of Washington, Seattle, WA, USA. mann@gs.washington.edu</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
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<orgName type="university">Université de Washington</orgName>
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<series><title level="j">Bioinformatics (Oxford, England)</title>
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<term>Base Sequence</term>
<term>Binding Sites</term>
<term>DNA (genetics)</term>
<term>DNA Primers (genetics)</term>
<term>Databases, Genetic</term>
<term>In Situ Hybridization (methods)</term>
<term>Molecular Sequence Data</term>
<term>Sequence Alignment (methods)</term>
<term>Sequence Analysis, DNA (methods)</term>
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<keywords scheme="KwdFr" xml:lang="fr"><term>ADN (génétique)</term>
<term>Algorithmes</term>
<term>Alignement de séquences ()</term>
<term>Amorces ADN (génétique)</term>
<term>Analyse de séquence d'ADN ()</term>
<term>Appariement de bases (génétique)</term>
<term>Bases de données génétiques</term>
<term>Données de séquences moléculaires</term>
<term>Hybridation in situ ()</term>
<term>Sites de fixation</term>
<term>Séquence nucléotidique</term>
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<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA</term>
<term>DNA Primers</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Base Pairing</term>
</keywords>
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<term>Amorces ADN</term>
<term>Appariement de bases</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>In Situ Hybridization</term>
<term>Sequence Alignment</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Algorithms</term>
<term>Base Sequence</term>
<term>Binding Sites</term>
<term>Databases, Genetic</term>
<term>Molecular Sequence Data</term>
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<term>Alignement de séquences</term>
<term>Analyse de séquence d'ADN</term>
<term>Bases de données génétiques</term>
<term>Données de séquences moléculaires</term>
<term>Hybridation in situ</term>
<term>Sites de fixation</term>
<term>Séquence nucléotidique</term>
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<front><div type="abstract" xml:lang="en">The specific hybridization of complementary DNA molecules underlies many widely used molecular biology assays, including the polymerase chain reaction and various types of microarray analysis. In order for such an assay to work well, the primer or probe must bind to its intended target, without also binding to additional sequences in the reaction mixture. For any given probe or primer, potential non-specific binding partners can be identified using state-of-the-art models of DNA binding stability. Unfortunately, these models rely on dynamic programming algorithms that are too slow to apply on a genomic scale.</div>
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