Software for automated analysis of DNA fingerprinting gels.
Identifieur interne : 004384 ( Main/Exploration ); précédent : 004383; suivant : 004385Software for automated analysis of DNA fingerprinting gels.
Auteurs : Daniel R. Fuhrmann [États-Unis] ; Martin I. Krzywinski ; Readman Chiu ; Parvaneh Saeedi ; Jacqueline E. Schein ; Ian E. Bosdet ; Asif Chinwalla ; Ladeana W. Hillier ; Robert H. Waterston ; John D. Mcpherson ; Steven J M. Jones ; Marco A. MarraSource :
- Genome research [ 1088-9051 ] ; 2003.
Descripteurs français
- KwdFr :
- MESH :
- génétique : ADN, Chromosomes artificiels de bactérie.
- méthodes : Profilage d'ADN.
- Agarose, Animaux, Bovins, Gels, Logiciel, Modèles chimiques, Rats, Souris.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA.
- genetics : Chromosomes, Artificial, Bacterial.
- methods : DNA Fingerprinting.
- Animals, Cattle, Gels, Mice, Models, Chemical, Rats, Sepharose, Software.
Abstract
Here we describe software tools for the automated detection of DNA restriction fragments resolved on agarose fingerprinting gels. We present a mathematical model for the location and shape of the restriction fragments as a function of fragment size, with model parameters determined empirically from "marker" lanes containing molecular size standards. Automated identification of restriction fragments involves several steps, including: image preprocessing, to put the data in a form consistent with a linear model; marker lane analysis, for determination of the model parameters; and data lane analysis, a procedure for detecting restriction fragment multiplets while simultaneously determining the amplitude curve that describes restriction fragment amplitude as a function of mobility. In validation experiments conducted on fingerprinted and sequenced Bacterial Artificial Chromosome (BAC) clones, sensitivity and specificity of restriction fragment identification exceeded 96% on restriction fragments ranging in size from 600 base pairs (bp) to 30,000 bp. The integrated suite of software tools, written in MATLAB and collectively called BandLeader, is in use at the BC Cancer Agency Genome Sciences Centre (GSC) and the Washington University Genome Sequencing Center, and has been provided to the Wellcome Trust Sanger Institute and the Whitehead Institute. Employed in a production mode at the GSC, BandLeader has been used to perform automated restriction fragment identification for more than 850,000 BAC clones for mouse, rat, bovine, and poplar fingerprint mapping projects.
DOI: 10.1101/gr.904303
PubMed: 12727910
PubMed Central: PMC430903
Affiliations:
Links toward previous steps (curation, corpus...)
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Krzywinski</name></author><author><name sortKey="Chiu, Readman" sort="Chiu, Readman" uniqKey="Chiu R" first="Readman" last="Chiu">Readman Chiu</name></author><author><name sortKey="Saeedi, Parvaneh" sort="Saeedi, Parvaneh" uniqKey="Saeedi P" first="Parvaneh" last="Saeedi">Parvaneh Saeedi</name></author><author><name sortKey="Schein, Jacqueline E" sort="Schein, Jacqueline E" uniqKey="Schein J" first="Jacqueline E" last="Schein">Jacqueline E. Schein</name></author><author><name sortKey="Bosdet, Ian E" sort="Bosdet, Ian E" uniqKey="Bosdet I" first="Ian E" last="Bosdet">Ian E. Bosdet</name></author><author><name sortKey="Chinwalla, Asif" sort="Chinwalla, Asif" uniqKey="Chinwalla A" first="Asif" last="Chinwalla">Asif Chinwalla</name></author><author><name sortKey="Hillier, Ladeana W" sort="Hillier, Ladeana W" uniqKey="Hillier L" first="Ladeana W" last="Hillier">Ladeana W. Hillier</name></author><author><name sortKey="Waterston, Robert H" sort="Waterston, Robert H" uniqKey="Waterston R" first="Robert H" last="Waterston">Robert H. Waterston</name></author><author><name sortKey="Mcpherson, John D" sort="Mcpherson, John D" uniqKey="Mcpherson J" first="John D" last="Mcpherson">John D. Mcpherson</name></author><author><name sortKey="Jones, Steven J M" sort="Jones, Steven J M" uniqKey="Jones S" first="Steven J M" last="Jones">Steven J M. Jones</name></author><author><name sortKey="Marra, Marco A" sort="Marra, Marco A" uniqKey="Marra M" first="Marco A" last="Marra">Marco A. Marra</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2003">2003</date><idno type="RBID">pubmed:12727910</idno><idno type="pmid">12727910</idno><idno type="doi">10.1101/gr.904303</idno><idno type="pmc">PMC430903</idno><idno type="wicri:Area/Main/Corpus">004470</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">004470</idno><idno type="wicri:Area/Main/Curation">004470</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">004470</idno><idno type="wicri:Area/Main/Exploration">004470</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Software for automated analysis of DNA fingerprinting gels.</title><author><name sortKey="Fuhrmann, Daniel R" sort="Fuhrmann, Daniel R" uniqKey="Fuhrmann D" first="Daniel R" last="Fuhrmann">Daniel R. Fuhrmann</name><affiliation wicri:level="1"><nlm:affiliation>Department of Electrical Engineering, Washington University, St. Louis, Missouri 63130, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Electrical Engineering, Washington University, St. Louis, Missouri 63130</wicri:regionArea><wicri:noRegion>Missouri 63130</wicri:noRegion></affiliation></author><author><name sortKey="Krzywinski, Martin I" sort="Krzywinski, Martin I" uniqKey="Krzywinski M" first="Martin I" last="Krzywinski">Martin I. Krzywinski</name></author><author><name sortKey="Chiu, Readman" sort="Chiu, Readman" uniqKey="Chiu R" first="Readman" last="Chiu">Readman Chiu</name></author><author><name sortKey="Saeedi, Parvaneh" sort="Saeedi, Parvaneh" uniqKey="Saeedi P" first="Parvaneh" last="Saeedi">Parvaneh Saeedi</name></author><author><name sortKey="Schein, Jacqueline E" sort="Schein, Jacqueline E" uniqKey="Schein J" first="Jacqueline E" last="Schein">Jacqueline E. Schein</name></author><author><name sortKey="Bosdet, Ian E" sort="Bosdet, Ian E" uniqKey="Bosdet I" first="Ian E" last="Bosdet">Ian E. Bosdet</name></author><author><name sortKey="Chinwalla, Asif" sort="Chinwalla, Asif" uniqKey="Chinwalla A" first="Asif" last="Chinwalla">Asif Chinwalla</name></author><author><name sortKey="Hillier, Ladeana W" sort="Hillier, Ladeana W" uniqKey="Hillier L" first="Ladeana W" last="Hillier">Ladeana W. Hillier</name></author><author><name sortKey="Waterston, Robert H" sort="Waterston, Robert H" uniqKey="Waterston R" first="Robert H" last="Waterston">Robert H. Waterston</name></author><author><name sortKey="Mcpherson, John D" sort="Mcpherson, John D" uniqKey="Mcpherson J" first="John D" last="Mcpherson">John D. Mcpherson</name></author><author><name sortKey="Jones, Steven J M" sort="Jones, Steven J M" uniqKey="Jones S" first="Steven J M" last="Jones">Steven J M. Jones</name></author><author><name sortKey="Marra, Marco A" sort="Marra, Marco A" uniqKey="Marra M" first="Marco A" last="Marra">Marco A. Marra</name></author></analytic><series><title level="j">Genome research</title><idno type="ISSN">1088-9051</idno><imprint><date when="2003" type="published">2003</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals (MeSH)</term><term>Cattle (MeSH)</term><term>Chromosomes, Artificial, Bacterial (genetics)</term><term>DNA (genetics)</term><term>DNA Fingerprinting (methods)</term><term>Gels (MeSH)</term><term>Mice (MeSH)</term><term>Models, Chemical (MeSH)</term><term>Rats (MeSH)</term><term>Sepharose (MeSH)</term><term>Software (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN (génétique)</term><term>Agarose (MeSH)</term><term>Animaux (MeSH)</term><term>Bovins (MeSH)</term><term>Chromosomes artificiels de bactérie (génétique)</term><term>Gels (MeSH)</term><term>Logiciel (MeSH)</term><term>Modèles chimiques (MeSH)</term><term>Profilage d'ADN (méthodes)</term><term>Rats (MeSH)</term><term>Souris (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Chromosomes, Artificial, Bacterial</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN</term><term>Chromosomes artificiels de bactérie</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>DNA Fingerprinting</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Profilage d'ADN</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Cattle</term><term>Gels</term><term>Mice</term><term>Models, Chemical</term><term>Rats</term><term>Sepharose</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Agarose</term><term>Animaux</term><term>Bovins</term><term>Gels</term><term>Logiciel</term><term>Modèles chimiques</term><term>Rats</term><term>Souris</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Here we describe software tools for the automated detection of DNA restriction fragments resolved on agarose fingerprinting gels. We present a mathematical model for the location and shape of the restriction fragments as a function of fragment size, with model parameters determined empirically from "marker" lanes containing molecular size standards. Automated identification of restriction fragments involves several steps, including: image preprocessing, to put the data in a form consistent with a linear model; marker lane analysis, for determination of the model parameters; and data lane analysis, a procedure for detecting restriction fragment multiplets while simultaneously determining the amplitude curve that describes restriction fragment amplitude as a function of mobility. In validation experiments conducted on fingerprinted and sequenced Bacterial Artificial Chromosome (BAC) clones, sensitivity and specificity of restriction fragment identification exceeded 96% on restriction fragments ranging in size from 600 base pairs (bp) to 30,000 bp. The integrated suite of software tools, written in MATLAB and collectively called BandLeader, is in use at the BC Cancer Agency Genome Sciences Centre (GSC) and the Washington University Genome Sequencing Center, and has been provided to the Wellcome Trust Sanger Institute and the Whitehead Institute. Employed in a production mode at the GSC, BandLeader has been used to perform automated restriction fragment identification for more than 850,000 BAC clones for mouse, rat, bovine, and poplar fingerprint mapping projects.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">12727910</PMID><DateCompleted><Year>2003</Year><Month>06</Month><Day>06</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">1088-9051</ISSN><JournalIssue CitedMedium="Print"><Volume>13</Volume><Issue>5</Issue><PubDate><Year>2003</Year><Month>May</Month></PubDate></JournalIssue><Title>Genome research</Title><ISOAbbreviation>Genome Res</ISOAbbreviation></Journal><ArticleTitle>Software for automated analysis of DNA fingerprinting gels.</ArticleTitle><Pagination><MedlinePgn>940-53</MedlinePgn></Pagination><Abstract><AbstractText>Here we describe software tools for the automated detection of DNA restriction fragments resolved on agarose fingerprinting gels. We present a mathematical model for the location and shape of the restriction fragments as a function of fragment size, with model parameters determined empirically from "marker" lanes containing molecular size standards. Automated identification of restriction fragments involves several steps, including: image preprocessing, to put the data in a form consistent with a linear model; marker lane analysis, for determination of the model parameters; and data lane analysis, a procedure for detecting restriction fragment multiplets while simultaneously determining the amplitude curve that describes restriction fragment amplitude as a function of mobility. In validation experiments conducted on fingerprinted and sequenced Bacterial Artificial Chromosome (BAC) clones, sensitivity and specificity of restriction fragment identification exceeded 96% on restriction fragments ranging in size from 600 base pairs (bp) to 30,000 bp. The integrated suite of software tools, written in MATLAB and collectively called BandLeader, is in use at the BC Cancer Agency Genome Sciences Centre (GSC) and the Washington University Genome Sequencing Center, and has been provided to the Wellcome Trust Sanger Institute and the Whitehead Institute. Employed in a production mode at the GSC, BandLeader has been used to perform automated restriction fragment identification for more than 850,000 BAC clones for mouse, rat, bovine, and poplar fingerprint mapping projects.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Fuhrmann</LastName><ForeName>Daniel R</ForeName><Initials>DR</Initials><AffiliationInfo><Affiliation>Department of Electrical Engineering, Washington University, St. Louis, Missouri 63130, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Krzywinski</LastName><ForeName>Martin I</ForeName><Initials>MI</Initials></Author><Author ValidYN="Y"><LastName>Chiu</LastName><ForeName>Readman</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Saeedi</LastName><ForeName>Parvaneh</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Schein</LastName><ForeName>Jacqueline E</ForeName><Initials>JE</Initials></Author><Author ValidYN="Y"><LastName>Bosdet</LastName><ForeName>Ian E</ForeName><Initials>IE</Initials></Author><Author ValidYN="Y"><LastName>Chinwalla</LastName><ForeName>Asif</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Hillier</LastName><ForeName>LaDeana W</ForeName><Initials>LW</Initials></Author><Author ValidYN="Y"><LastName>Waterston</LastName><ForeName>Robert H</ForeName><Initials>RH</Initials></Author><Author ValidYN="Y"><LastName>McPherson</LastName><ForeName>John D</ForeName><Initials>JD</Initials></Author><Author ValidYN="Y"><LastName>Jones</LastName><ForeName>Steven J M</ForeName><Initials>SJ</Initials></Author><Author ValidYN="Y"><LastName>Marra</LastName><ForeName>Marco A</ForeName><Initials>MA</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>U01 HG002155</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>1-U01-HG02155</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>1U01-HG02042</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013487">Research Support, U.S. Gov't, P.H.S.</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Genome Res</MedlineTA><NlmUniqueID>9518021</NlmUniqueID><ISSNLinking>1088-9051</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005782">Gels</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical><Chemical><RegistryNumber>9012-36-6</RegistryNumber><NameOfSubstance UI="D012685">Sepharose</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002417" MajorTopicYN="N">Cattle</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D022202" MajorTopicYN="N">Chromosomes, Artificial, Bacterial</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016172" MajorTopicYN="N">DNA Fingerprinting</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005782" MajorTopicYN="Y">Gels</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D051379" MajorTopicYN="N">Mice</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008956" MajorTopicYN="N">Models, Chemical</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D051381" MajorTopicYN="N">Rats</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012685" MajorTopicYN="N">Sepharose</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2003</Year><Month>5</Month><Day>3</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2003</Year><Month>6</Month><Day>7</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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Bosdet</name><name sortKey="Chinwalla, Asif" sort="Chinwalla, Asif" uniqKey="Chinwalla A" first="Asif" last="Chinwalla">Asif Chinwalla</name><name sortKey="Chiu, Readman" sort="Chiu, Readman" uniqKey="Chiu R" first="Readman" last="Chiu">Readman Chiu</name><name sortKey="Hillier, Ladeana W" sort="Hillier, Ladeana W" uniqKey="Hillier L" first="Ladeana W" last="Hillier">Ladeana W. Hillier</name><name sortKey="Jones, Steven J M" sort="Jones, Steven J M" uniqKey="Jones S" first="Steven J M" last="Jones">Steven J M. Jones</name><name sortKey="Krzywinski, Martin I" sort="Krzywinski, Martin I" uniqKey="Krzywinski M" first="Martin I" last="Krzywinski">Martin I. Krzywinski</name><name sortKey="Marra, Marco A" sort="Marra, Marco A" uniqKey="Marra M" first="Marco A" last="Marra">Marco A. Marra</name><name sortKey="Mcpherson, John D" sort="Mcpherson, John D" uniqKey="Mcpherson J" first="John D" last="Mcpherson">John D. Mcpherson</name><name sortKey="Saeedi, Parvaneh" sort="Saeedi, Parvaneh" uniqKey="Saeedi P" first="Parvaneh" last="Saeedi">Parvaneh Saeedi</name><name sortKey="Schein, Jacqueline E" sort="Schein, Jacqueline E" uniqKey="Schein J" first="Jacqueline E" last="Schein">Jacqueline E. Schein</name><name sortKey="Waterston, Robert H" sort="Waterston, Robert H" uniqKey="Waterston R" first="Robert H" last="Waterston">Robert H. Waterston</name></noCountry><country name="États-Unis"><noRegion><name sortKey="Fuhrmann, Daniel R" sort="Fuhrmann, Daniel R" uniqKey="Fuhrmann D" first="Daniel R" last="Fuhrmann">Daniel R. Fuhrmann</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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