Efficient identification of DNA hybridization partners in a sequence database.
Identifieur interne : 000454 ( Ncbi/Merge ); précédent : 000453; suivant : 000455Efficient 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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<author><name sortKey="Mann, Tobias P" sort="Mann, Tobias P" uniqKey="Mann T" first="Tobias P" last="Mann">Tobias P. Mann</name>
<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>
<wicri:regionArea>Department of Genome Sciences, University of Washington, Seattle, WA</wicri:regionArea>
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<orgName type="university">Université de Washington</orgName>
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<author><name sortKey="Noble, William Stafford" sort="Noble, William Stafford" uniqKey="Noble W" first="William Stafford" last="Noble">William Stafford Noble</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">Efficient identification of DNA hybridization partners in a sequence database.</title>
<author><name sortKey="Mann, Tobias P" sort="Mann, Tobias P" uniqKey="Mann T" first="Tobias P" last="Mann">Tobias P. Mann</name>
<affiliation wicri:level="4"><nlm:affiliation>Department of Genome Sciences, University of Washington, Seattle, WA, USA. mann@gs.washington.edu</nlm:affiliation>
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<series><title level="j">Bioinformatics (Oxford, England)</title>
<idno type="eISSN">1367-4811</idno>
<imprint><date when="2006" type="published">2006</date>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term>
<term>Base Pairing (genetics)</term>
<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>
</keywords>
<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>
</keywords>
<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>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN</term>
<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>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term>
<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>
</keywords>
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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>
</front>
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<DateCompleted><Year>2006</Year>
<Month>10</Month>
<Day>05</Day>
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<DateRevised><Year>2019</Year>
<Month>12</Month>
<Day>10</Day>
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<Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN>
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<Issue>14</Issue>
<PubDate><Year>2006</Year>
<Month>Jul</Month>
<Day>15</Day>
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<Title>Bioinformatics (Oxford, England)</Title>
<ISOAbbreviation>Bioinformatics</ISOAbbreviation>
</Journal>
<ArticleTitle>Efficient identification of DNA hybridization partners in a sequence database.</ArticleTitle>
<Pagination><MedlinePgn>e350-8</MedlinePgn>
</Pagination>
<Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">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.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">We present an algorithm that efficiently scans a DNA database for short (approximately 20-30 base) sequences that will bind to a query sequence. We use a filtering approach, in which a series of increasingly stringent filters is applied to a set of candidate k-mers. The k-mers that pass all filters are then located in the sequence database using a precomputed index, and an accurate model of DNA binding stability is applied to the sequence surrounding each of the k-mer occurrences. This approach reduces the time to identify all binding partners for a given DNA sequence in human genomic DNA by approximately three orders of magnitude, from two days for the ENCODE regions to less than one minute for typical queries. Our approach is scalable to large DNA sequences. Our method can scan the human genome for medium strength binding sites to a candidate PCR primer in an average of 34.5 minutes.</AbstractText>
<AbstractText Label="AVAILABILITY" NlmCategory="BACKGROUND">Software implementing the algorithms described here is available at http://noble.gs.washington.edu/proj/dna-binding.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Mann</LastName>
<ForeName>Tobias P</ForeName>
<Initials>TP</Initials>
<AffiliationInfo><Affiliation>Department of Genome Sciences, University of Washington, Seattle, WA, USA. mann@gs.washington.edu</Affiliation>
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<Author ValidYN="Y"><LastName>Noble</LastName>
<ForeName>William Stafford</ForeName>
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<Language>eng</Language>
<GrantList CompleteYN="Y"><Grant><GrantID>R01 GM071923</GrantID>
<Acronym>GM</Acronym>
<Agency>NIGMS NIH HHS</Agency>
<Country>United States</Country>
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<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D017931">DNA Primers</NameOfSubstance>
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<Chemical><RegistryNumber>9007-49-2</RegistryNumber>
<NameOfSubstance UI="D004247">DNA</NameOfSubstance>
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<MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="Y">Algorithms</DescriptorName>
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<MeshHeading><DescriptorName UI="D020029" MajorTopicYN="N">Base Pairing</DescriptorName>
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<MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName>
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<MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName>
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<MeshHeading><DescriptorName UI="D017931" MajorTopicYN="N">DNA Primers</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D030541" MajorTopicYN="Y">Databases, Genetic</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017403" MajorTopicYN="N">In Situ Hybridization</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016415" MajorTopicYN="N">Sequence Alignment</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName>
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