JBrowse: a dynamic web platform for genome visualization and analysis
Identifieur interne : 000025 ( Main/Exploration ); précédent : 000024; suivant : 000026JBrowse: a dynamic web platform for genome visualization and analysis
Auteurs : Robert Buels [États-Unis] ; Eric Yao [États-Unis] ; Colin M. Diesh ; Richard D. Hayes [États-Unis] ; Monica Munoz-Torres [États-Unis] ; Gregg Helt [États-Unis] ; David M. Goodstein [États-Unis] ; Christine G. Elsik ; Suzanna E. Lewis [États-Unis] ; Lincoln Stein ; Ian H. Holmes [États-Unis]Source :
- Genome Biology [ 1474-7596 ] ; 2016.
Abstract
JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page.
Overall improvements to speed and scalability are accompanied by specific enhancements that support complex interactive queries on large track sets. Analysis functions can readily be added using the plugin framework; most visual aspects of tracks can also be customized, along with clicks, mouseovers, menus, and popup boxes. JBrowse can also be used to browse local annotation files offline and to generate high-resolution figures for publication.
JBrowse is a mature web application suitable for genome visualization and analysis.
Url:
DOI: 10.1186/s13059-016-0924-1
PubMed: 27072794
PubMed Central: 4830012
Affiliations:
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Goodstein</name><affiliation wicri:level="2"><nlm:aff id="Aff3">Lawrence Berkeley National Laboratory, Berkeley, California USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Lawrence Berkeley National Laboratory, Berkeley</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff6">US Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>US Department of Energy, Joint Genome Institute, Walnut Creek</wicri:cityArea></affiliation></author><author><name sortKey="Elsik, Christine G" sort="Elsik, Christine G" uniqKey="Elsik C" first="Christine G." last="Elsik">Christine G. 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Lewis</name><affiliation wicri:level="2"><nlm:aff id="Aff3">Lawrence Berkeley National Laboratory, Berkeley, California USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Lawrence Berkeley National Laboratory, Berkeley</wicri:cityArea></affiliation></author><author><name sortKey="Stein, Lincoln" sort="Stein, Lincoln" uniqKey="Stein L" first="Lincoln" last="Stein">Lincoln Stein</name><affiliation><nlm:aff id="Aff5">Ontario Institute of Cancer Research, Toronto, Ontario Canada</nlm:aff><wicri:noCountry code="subfield">Ontario Canada</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff7">Department of Molecular Genetics, University of Toronto, Toronto, Ontario Canada</nlm:aff><wicri:noCountry code="subfield">Ontario Canada</wicri:noCountry></affiliation></author><author><name sortKey="Holmes, Ian H" sort="Holmes, Ian H" uniqKey="Holmes I" first="Ian H." last="Holmes">Ian H. Holmes</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Department of Bioengineering, University of California, Berkeley, California USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Department of Bioengineering, University of California, Berkeley</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff3">Lawrence Berkeley National Laboratory, Berkeley, California USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Lawrence Berkeley National Laboratory, Berkeley</wicri:cityArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27072794</idno><idno type="pmc">4830012</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4830012</idno><idno type="RBID">PMC:4830012</idno><idno type="doi">10.1186/s13059-016-0924-1</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000181</idno><idno type="wicri:Area/Pmc/Curation">000181</idno><idno type="wicri:Area/Pmc/Checkpoint">000023</idno><idno type="wicri:Area/Ncbi/Merge">000724</idno><idno type="wicri:Area/Ncbi/Curation">000724</idno><idno type="wicri:Area/Ncbi/Checkpoint">000724</idno><idno type="wicri:doubleKey">1474-7596:2016:Buels R:jbrowse:a:dynamic</idno><idno type="wicri:Area/Main/Merge">000025</idno><idno type="wicri:Area/Main/Curation">000025</idno><idno type="wicri:Area/Main/Exploration">000025</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">JBrowse: a dynamic web platform for genome visualization and analysis</title><author><name sortKey="Buels, Robert" sort="Buels, Robert" uniqKey="Buels R" first="Robert" last="Buels">Robert Buels</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Department of Bioengineering, University of California, Berkeley, California USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Department of Bioengineering, University of California, Berkeley</wicri:cityArea></affiliation></author><author><name sortKey="Yao, Eric" sort="Yao, Eric" uniqKey="Yao E" first="Eric" last="Yao">Eric Yao</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Department of Bioengineering, University of California, Berkeley, California USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Department of Bioengineering, University of California, Berkeley</wicri:cityArea></affiliation></author><author><name sortKey="Diesh, Colin M" sort="Diesh, Colin M" uniqKey="Diesh C" first="Colin M." last="Diesh">Colin M. Diesh</name><affiliation><nlm:aff id="Aff2">Division of Animal Sciences, University of Missouri, Columbia, Missouri USA</nlm:aff><wicri:noCountry code="subfield">Missouri USA</wicri:noCountry></affiliation></author><author><name sortKey="Hayes, Richard D" sort="Hayes, Richard D" uniqKey="Hayes R" first="Richard D." last="Hayes">Richard D. Hayes</name><affiliation wicri:level="2"><nlm:aff id="Aff3">Lawrence Berkeley National Laboratory, Berkeley, California USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Lawrence Berkeley National Laboratory, Berkeley</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff6">US Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>US Department of Energy, Joint Genome Institute, Walnut Creek</wicri:cityArea></affiliation></author><author><name sortKey="Munoz Torres, Monica" sort="Munoz Torres, Monica" uniqKey="Munoz Torres M" first="Monica" last="Munoz-Torres">Monica Munoz-Torres</name><affiliation wicri:level="2"><nlm:aff id="Aff3">Lawrence Berkeley National Laboratory, Berkeley, California USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Lawrence Berkeley National Laboratory, Berkeley</wicri:cityArea></affiliation></author><author><name sortKey="Helt, Gregg" sort="Helt, Gregg" uniqKey="Helt G" first="Gregg" last="Helt">Gregg Helt</name><affiliation wicri:level="2"><nlm:aff id="Aff3">Lawrence Berkeley National Laboratory, Berkeley, California USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Lawrence Berkeley National Laboratory, Berkeley</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff4">Current affiliation: Genomancer Consulting, Healdsburg, California USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Current affiliation: Genomancer Consulting, Healdsburg</wicri:cityArea></affiliation></author><author><name sortKey="Goodstein, David M" sort="Goodstein, David M" uniqKey="Goodstein D" first="David M." last="Goodstein">David M. Goodstein</name><affiliation wicri:level="2"><nlm:aff id="Aff3">Lawrence Berkeley National Laboratory, Berkeley, California USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Lawrence Berkeley National Laboratory, Berkeley</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff6">US Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>US Department of Energy, Joint Genome Institute, Walnut Creek</wicri:cityArea></affiliation></author><author><name sortKey="Elsik, Christine G" sort="Elsik, Christine G" uniqKey="Elsik C" first="Christine G." last="Elsik">Christine G. Elsik</name><affiliation><nlm:aff id="Aff2">Division of Animal Sciences, University of Missouri, Columbia, Missouri USA</nlm:aff><wicri:noCountry code="subfield">Missouri USA</wicri:noCountry></affiliation></author><author><name sortKey="Lewis, Suzanna E" sort="Lewis, Suzanna E" uniqKey="Lewis S" first="Suzanna E." last="Lewis">Suzanna E. Lewis</name><affiliation wicri:level="2"><nlm:aff id="Aff3">Lawrence Berkeley National Laboratory, Berkeley, California USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Lawrence Berkeley National Laboratory, Berkeley</wicri:cityArea></affiliation></author><author><name sortKey="Stein, Lincoln" sort="Stein, Lincoln" uniqKey="Stein L" first="Lincoln" last="Stein">Lincoln Stein</name><affiliation><nlm:aff id="Aff5">Ontario Institute of Cancer Research, Toronto, Ontario Canada</nlm:aff><wicri:noCountry code="subfield">Ontario Canada</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff7">Department of Molecular Genetics, University of Toronto, Toronto, Ontario Canada</nlm:aff><wicri:noCountry code="subfield">Ontario Canada</wicri:noCountry></affiliation></author><author><name sortKey="Holmes, Ian H" sort="Holmes, Ian H" uniqKey="Holmes I" first="Ian H." last="Holmes">Ian H. Holmes</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Department of Bioengineering, University of California, Berkeley, California USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Department of Bioengineering, University of California, Berkeley</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="Aff3">Lawrence Berkeley National Laboratory, Berkeley, California USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Lawrence Berkeley National Laboratory, Berkeley</wicri:cityArea></affiliation></author></analytic><series><title level="j">Genome Biology</title><idno type="ISSN">1474-7596</idno><idno type="eISSN">1474-760X</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page.</p></sec><sec><title>Results</title><p>Overall improvements to speed and scalability are accompanied by specific enhancements that support complex interactive queries on large track sets. Analysis functions can readily be added using the plugin framework; most visual aspects of tracks can also be customized, along with clicks, mouseovers, menus, and popup boxes. JBrowse can also be used to browse local annotation files offline and to generate high-resolution figures for publication.</p></sec><sec><title>Conclusions</title><p>JBrowse is a mature web application suitable for genome visualization and analysis.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Skinner, Me" uniqKey="Skinner M">ME Skinner</name></author><author><name sortKey="Uzilov, Av" uniqKey="Uzilov A">AV Uzilov</name></author><author><name sortKey="Stein, Ld" uniqKey="Stein L">LD Stein</name></author><author><name sortKey="Mungall, Cj" uniqKey="Mungall C">CJ Mungall</name></author><author><name sortKey="Holmes, Ih" uniqKey="Holmes I">IH Holmes</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Westesson, O" uniqKey="Westesson O">O Westesson</name></author><author><name sortKey="Skinner, M" uniqKey="Skinner M">M Skinner</name></author><author><name 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uniqKey="Fennell T">T Fennell</name></author><author><name sortKey="Ruan, J" uniqKey="Ruan J">J Ruan</name></author><author><name sortKey="Homer, N" uniqKey="Homer N">N Homer</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Californie</li></region></list><tree><noCountry><name sortKey="Diesh, Colin M" sort="Diesh, Colin M" uniqKey="Diesh C" first="Colin M." last="Diesh">Colin M. Diesh</name><name sortKey="Elsik, Christine G" sort="Elsik, Christine G" uniqKey="Elsik C" first="Christine G." last="Elsik">Christine G. Elsik</name><name sortKey="Stein, Lincoln" sort="Stein, Lincoln" uniqKey="Stein L" first="Lincoln" last="Stein">Lincoln Stein</name></noCountry><country name="États-Unis"><region name="Californie"><name sortKey="Buels, Robert" sort="Buels, Robert" uniqKey="Buels R" first="Robert" last="Buels">Robert Buels</name></region><name sortKey="Goodstein, David M" sort="Goodstein, David M" uniqKey="Goodstein D" first="David M." last="Goodstein">David M. Goodstein</name><name sortKey="Goodstein, David M" sort="Goodstein, David M" uniqKey="Goodstein D" first="David M." last="Goodstein">David M. Goodstein</name><name sortKey="Hayes, Richard D" sort="Hayes, Richard D" uniqKey="Hayes R" first="Richard D." last="Hayes">Richard D. Hayes</name><name sortKey="Hayes, Richard D" sort="Hayes, Richard D" uniqKey="Hayes R" first="Richard D." last="Hayes">Richard D. Hayes</name><name sortKey="Helt, Gregg" sort="Helt, Gregg" uniqKey="Helt G" first="Gregg" last="Helt">Gregg Helt</name><name sortKey="Helt, Gregg" sort="Helt, Gregg" uniqKey="Helt G" first="Gregg" last="Helt">Gregg Helt</name><name sortKey="Holmes, Ian H" sort="Holmes, Ian H" uniqKey="Holmes I" first="Ian H." last="Holmes">Ian H. Holmes</name><name sortKey="Holmes, Ian H" sort="Holmes, Ian H" uniqKey="Holmes I" first="Ian H." last="Holmes">Ian H. Holmes</name><name sortKey="Lewis, Suzanna E" sort="Lewis, Suzanna E" uniqKey="Lewis S" first="Suzanna E." last="Lewis">Suzanna E. Lewis</name><name sortKey="Munoz Torres, Monica" sort="Munoz Torres, Monica" uniqKey="Munoz Torres M" first="Monica" last="Munoz-Torres">Monica Munoz-Torres</name><name sortKey="Yao, Eric" sort="Yao, Eric" uniqKey="Yao E" first="Eric" last="Yao">Eric Yao</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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