Internet Contig Explorer (iCE)--a tool for visualizing clone fingerprint maps.
Identifieur interne : 004426 ( Main/Exploration ); précédent : 004425; suivant : 004427Internet Contig Explorer (iCE)--a tool for visualizing clone fingerprint maps.
Auteurs : Christopher D. Fjell [Canada] ; Ian Bosdet ; Jacqueline E. Schein ; Steven J M. Jones ; Marco A. MarraSource :
- Genome research [ 1088-9051 ] ; 2003.
Descripteurs français
- KwdFr :
- ADN des helminthes (génétique), ADN des plantes (génétique), Animaux (MeSH), Arabidopsis (génétique), Caenorhabditis (génétique), Caenorhabditis elegans (génétique), Cartographie de contigs (méthodes), Clonage moléculaire (méthodes), Humains (MeSH), Internet (MeSH), Logiciel (MeSH), Oryza (génétique), Profilage d'ADN (méthodes), Rats (MeSH), Souris (MeSH).
- MESH :
- génétique : ADN des helminthes, ADN des plantes, Arabidopsis, Caenorhabditis, Caenorhabditis elegans, Oryza.
- méthodes : Cartographie de contigs, Clonage moléculaire, Profilage d'ADN.
- Animaux, Humains, Internet, Logiciel, Rats, Souris.
English descriptors
- KwdEn :
- Animals (MeSH), Arabidopsis (genetics), Caenorhabditis (genetics), Caenorhabditis elegans (genetics), Cloning, Molecular (methods), Contig Mapping (methods), DNA Fingerprinting (methods), DNA, Helminth (genetics), DNA, Plant (genetics), Humans (MeSH), Internet (MeSH), Mice (MeSH), Oryza (genetics), Rats (MeSH), Software (MeSH).
- MESH :
- chemical , genetics : DNA, Helminth, DNA, Plant.
- genetics : Arabidopsis, Caenorhabditis, Caenorhabditis elegans, Oryza.
- methods : Cloning, Molecular, Contig Mapping, DNA Fingerprinting.
- Animals, Humans, Internet, Mice, Rats, Software.
Abstract
Fingerprinted clone physical maps have proven useful in various applications, supporting both whole-genome and region-specific DNA sequencing as well as gene cloning studies. Fingerprint maps have been generated for several genomes, including those of human, mouse, rat, the nematodes Caenorhabditis elegans and Caenorhabditis briggsae, Arabidopsis thaliana and rice. Fingerprint maps of other genomes, including those of fungi, bacteria, poplar, and the cow, are being generated. The increasing use of fingerprint maps in genomic research has spawned a need in the research community for intuitive computer tools that facilitate viewing of the maps and the underlying fingerprint data. In this report we describe a new Java-based application called iCE (Internet Contig Explorer) that has been designed to provide views of fingerprint maps and associated data. Users can search for and display individual clones, contigs, clone fingerprints, clone insert sizes and markers. Users can also load into the software lists of particular clones of interest and view their fingerprints. iCE is being used at our Genome Centre to offer up to the research community views of the mouse, rat, bovine, C. briggsae, and several fungal genome bacterial artificial chromosome (BAC) fingerprint maps we have either completed or are currently constructing. We are also using iCE as part of the Rat Genome Sequencing Project to manage our provision of rat BAC clones for sequencing at the Human Genome Sequencing Center at the Baylor College of Medicine.
DOI: 10.1101/gr.819303
PubMed: 12799356
PubMed Central: PMC403654
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Schein</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:12799356</idno><idno type="pmid">12799356</idno><idno type="doi">10.1101/gr.819303</idno><idno type="pmc">PMC403654</idno><idno type="wicri:Area/Main/Corpus">004453</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">004453</idno><idno type="wicri:Area/Main/Curation">004453</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">004453</idno><idno type="wicri:Area/Main/Exploration">004453</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Internet Contig Explorer (iCE)--a tool for visualizing clone fingerprint maps.</title><author><name sortKey="Fjell, Christopher D" sort="Fjell, Christopher D" uniqKey="Fjell C" first="Christopher D" last="Fjell">Christopher D. Fjell</name><affiliation wicri:level="1"><nlm:affiliation>Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6</wicri:regionArea><wicri:noRegion>BC V5Z 4E6</wicri:noRegion></affiliation></author><author><name sortKey="Bosdet, Ian" sort="Bosdet, Ian" uniqKey="Bosdet I" first="Ian" last="Bosdet">Ian Bosdet</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="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>Arabidopsis (genetics)</term><term>Caenorhabditis (genetics)</term><term>Caenorhabditis elegans (genetics)</term><term>Cloning, Molecular (methods)</term><term>Contig Mapping (methods)</term><term>DNA Fingerprinting (methods)</term><term>DNA, Helminth (genetics)</term><term>DNA, Plant (genetics)</term><term>Humans (MeSH)</term><term>Internet (MeSH)</term><term>Mice (MeSH)</term><term>Oryza (genetics)</term><term>Rats (MeSH)</term><term>Software (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des helminthes (génétique)</term><term>ADN des plantes (génétique)</term><term>Animaux (MeSH)</term><term>Arabidopsis (génétique)</term><term>Caenorhabditis (génétique)</term><term>Caenorhabditis elegans (génétique)</term><term>Cartographie de contigs (méthodes)</term><term>Clonage moléculaire (méthodes)</term><term>Humains (MeSH)</term><term>Internet (MeSH)</term><term>Logiciel (MeSH)</term><term>Oryza (génétique)</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, Helminth</term><term>DNA, Plant</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Caenorhabditis</term><term>Caenorhabditis elegans</term><term>Oryza</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN des helminthes</term><term>ADN des plantes</term><term>Arabidopsis</term><term>Caenorhabditis</term><term>Caenorhabditis elegans</term><term>Oryza</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Cloning, Molecular</term><term>Contig Mapping</term><term>DNA Fingerprinting</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Cartographie de contigs</term><term>Clonage moléculaire</term><term>Profilage d'ADN</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Humans</term><term>Internet</term><term>Mice</term><term>Rats</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Humains</term><term>Internet</term><term>Logiciel</term><term>Rats</term><term>Souris</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Fingerprinted clone physical maps have proven useful in various applications, supporting both whole-genome and region-specific DNA sequencing as well as gene cloning studies. Fingerprint maps have been generated for several genomes, including those of human, mouse, rat, the nematodes Caenorhabditis elegans and Caenorhabditis briggsae, Arabidopsis thaliana and rice. Fingerprint maps of other genomes, including those of fungi, bacteria, poplar, and the cow, are being generated. The increasing use of fingerprint maps in genomic research has spawned a need in the research community for intuitive computer tools that facilitate viewing of the maps and the underlying fingerprint data. In this report we describe a new Java-based application called iCE (Internet Contig Explorer) that has been designed to provide views of fingerprint maps and associated data. Users can search for and display individual clones, contigs, clone fingerprints, clone insert sizes and markers. Users can also load into the software lists of particular clones of interest and view their fingerprints. iCE is being used at our Genome Centre to offer up to the research community views of the mouse, rat, bovine, C. briggsae, and several fungal genome bacterial artificial chromosome (BAC) fingerprint maps we have either completed or are currently constructing. We are also using iCE as part of the Rat Genome Sequencing Project to manage our provision of rat BAC clones for sequencing at the Human Genome Sequencing Center at the Baylor College of Medicine.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">12799356</PMID><DateCompleted><Year>2003</Year><Month>08</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>6A</Issue><PubDate><Year>2003</Year><Month>Jun</Month></PubDate></JournalIssue><Title>Genome research</Title><ISOAbbreviation>Genome Res</ISOAbbreviation></Journal><ArticleTitle>Internet Contig Explorer (iCE)--a tool for visualizing clone fingerprint maps.</ArticleTitle><Pagination><MedlinePgn>1244-9</MedlinePgn></Pagination><Abstract><AbstractText>Fingerprinted clone physical maps have proven useful in various applications, supporting both whole-genome and region-specific DNA sequencing as well as gene cloning studies. Fingerprint maps have been generated for several genomes, including those of human, mouse, rat, the nematodes Caenorhabditis elegans and Caenorhabditis briggsae, Arabidopsis thaliana and rice. Fingerprint maps of other genomes, including those of fungi, bacteria, poplar, and the cow, are being generated. The increasing use of fingerprint maps in genomic research has spawned a need in the research community for intuitive computer tools that facilitate viewing of the maps and the underlying fingerprint data. In this report we describe a new Java-based application called iCE (Internet Contig Explorer) that has been designed to provide views of fingerprint maps and associated data. Users can search for and display individual clones, contigs, clone fingerprints, clone insert sizes and markers. Users can also load into the software lists of particular clones of interest and view their fingerprints. iCE is being used at our Genome Centre to offer up to the research community views of the mouse, rat, bovine, C. briggsae, and several fungal genome bacterial artificial chromosome (BAC) fingerprint maps we have either completed or are currently constructing. We are also using iCE as part of the Rat Genome Sequencing Project to manage our provision of rat BAC clones for sequencing at the Human Genome Sequencing Center at the Baylor College of Medicine.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Fjell</LastName><ForeName>Christopher D</ForeName><Initials>CD</Initials><AffiliationInfo><Affiliation>Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4E6, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bosdet</LastName><ForeName>Ian</ForeName><Initials>I</Initials></Author><Author ValidYN="Y"><LastName>Schein</LastName><ForeName>Jacqueline E</ForeName><Initials>JE</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><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</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="D018509">DNA, Helminth</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName><QualifierName UI="Q000235" 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Jones</name><name sortKey="Marra, Marco A" sort="Marra, Marco A" uniqKey="Marra M" first="Marco A" last="Marra">Marco A. Marra</name><name sortKey="Schein, Jacqueline E" sort="Schein, Jacqueline E" uniqKey="Schein J" first="Jacqueline E" last="Schein">Jacqueline E. Schein</name></noCountry><country name="Canada"><noRegion><name sortKey="Fjell, Christopher D" sort="Fjell, Christopher D" uniqKey="Fjell C" first="Christopher D" last="Fjell">Christopher D. Fjell</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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