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
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 002236
- to stream PubMed, to step Curation: 002236
- to stream PubMed, to step Checkpoint: 002135
Links to Exploration step
pubmed:16873493Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><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><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genome Sciences, University of Washington, Seattle, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region><settlement type="city">Seattle</settlement></placeName><orgName type="university">Université de Washington</orgName></affiliation></author><author><name sortKey="Noble, William Stafford" sort="Noble, William Stafford" uniqKey="Noble W" first="William Stafford" last="Noble">William Stafford Noble</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2006">2006</date><idno type="RBID">pubmed:16873493</idno><idno type="pmid">16873493</idno><idno type="doi">10.1093/bioinformatics/btl240</idno><idno type="wicri:Area/PubMed/Corpus">002236</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002236</idno><idno type="wicri:Area/PubMed/Curation">002236</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002236</idno><idno type="wicri:Area/PubMed/Checkpoint">002135</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002135</idno><idno type="wicri:Area/Ncbi/Merge">000454</idno></publicationStmt><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><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genome Sciences, University of Washington, Seattle, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region><settlement type="city">Seattle</settlement></placeName><orgName type="university">Université de Washington</orgName></affiliation></author><author><name sortKey="Noble, William Stafford" sort="Noble, William Stafford" uniqKey="Noble W" first="William Stafford" last="Noble">William Stafford Noble</name></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><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></textClass></profileDesc></teiHeader><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></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16873493</PMID><DateCompleted><Year>2006</Year><Month>10</Month><Day>05</Day></DateCompleted><DateRevised><Year>2019</Year><Month>12</Month><Day>10</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><Volume>22</Volume><Issue>14</Issue><PubDate><Year>2006</Year><Month>Jul</Month><Day>15</Day></PubDate></JournalIssue><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></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Noble</LastName><ForeName>William Stafford</ForeName><Initials>WS</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R01 GM071923</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R33 HG003070</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>T32 HG00035</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D023362">Evaluation Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Bioinformatics</MedlineTA><NlmUniqueID>9808944</NlmUniqueID><ISSNLinking>1367-4803</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D017931">DNA Primers</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="Y">Algorithms</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020029" MajorTopicYN="N">Base Pairing</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><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><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2006</Year><Month>7</Month><Day>29</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2006</Year><Month>10</Month><Day>6</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2006</Year><Month>7</Month><Day>29</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">16873493</ArticleId><ArticleId IdType="pii">22/14/e350</ArticleId><ArticleId IdType="doi">10.1093/bioinformatics/btl240</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Washington (État)</li></region><settlement><li>Seattle</li></settlement><orgName><li>Université de Washington</li></orgName></list><tree><noCountry><name sortKey="Noble, William Stafford" sort="Noble, William Stafford" uniqKey="Noble W" first="William Stafford" last="Noble">William Stafford Noble</name></noCountry><country name="États-Unis"><region name="Washington (État)"><name sortKey="Mann, Tobias P" sort="Mann, Tobias P" uniqKey="Mann T" first="Tobias P" last="Mann">Tobias P. Mann</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Ncbi/Merge
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000454 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd -nk 000454 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Ncbi
|étape= Merge
|type= RBID
|clé= pubmed:16873493
|texte= Efficient identification of DNA hybridization partners in a sequence database.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/RBID.i -Sk "pubmed:16873493" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |