JBrowse: a dynamic web platform for genome visualization and analysis
Identifieur interne : 000023 ( Pmc/Checkpoint ); précédent : 000022; suivant : 000024JBrowse: 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:
Links toward previous steps (curation, corpus...)
Links to Exploration step
PMC:4830012Le document en format XML
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<author><name sortKey="Holmes, Ian H" sort="Holmes, Ian H" uniqKey="Holmes I" first="Ian H." last="Holmes">Ian H. Holmes</name>
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<series><title level="j">Genome Biology</title>
<idno type="ISSN">1474-7596</idno>
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<imprint><date when="2016">2016</date>
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<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 sortKey="Holmes, I" uniqKey="Holmes I">I Holmes</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Down, Ta" uniqKey="Down T">TA Down</name>
</author>
<author><name sortKey="Piipari, M" uniqKey="Piipari M">M Piipari</name>
</author>
<author><name sortKey="Hubbard, Tjp" uniqKey="Hubbard T">TJP Hubbard</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Kent, Wj" uniqKey="Kent W">WJ Kent</name>
</author>
<author><name sortKey="Sugnet, Cw" uniqKey="Sugnet C">CW Sugnet</name>
</author>
<author><name sortKey="Furey, Ts" uniqKey="Furey T">TS Furey</name>
</author>
<author><name sortKey="Roskin, Km" uniqKey="Roskin K">KM Roskin</name>
</author>
<author><name sortKey="Pringle, Th" uniqKey="Pringle T">TH Pringle</name>
</author>
<author><name sortKey="Zahler, Am" uniqKey="Zahler A">AM Zahler</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Stalker, J" uniqKey="Stalker J">J Stalker</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Stein, Ld" uniqKey="Stein L">LD Stein</name>
</author>
<author><name sortKey="Mungall, C" uniqKey="Mungall C">C Mungall</name>
</author>
<author><name sortKey="Shu, S" uniqKey="Shu S">S Shu</name>
</author>
<author><name sortKey="Caudy, M" uniqKey="Caudy M">M Caudy</name>
</author>
<author><name sortKey="Mangone, M" uniqKey="Mangone M">M Mangone</name>
</author>
<author><name sortKey="Day, A" uniqKey="Day A">A Day</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Robinson, Jt" uniqKey="Robinson J">JT Robinson</name>
</author>
<author><name sortKey="Thorvaldsd Ttir, H" uniqKey="Thorvaldsd Ttir H">H Thorvaldsdóttir</name>
</author>
<author><name sortKey="Winckler, W" uniqKey="Winckler W">W Winckler</name>
</author>
<author><name sortKey="Guttman, M" uniqKey="Guttman M">M Guttman</name>
</author>
<author><name sortKey="Lander, Es" uniqKey="Lander E">ES Lander</name>
</author>
<author><name sortKey="Getz, G" uniqKey="Getz G">G Getz</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Nicol, Jw" uniqKey="Nicol J">JW Nicol</name>
</author>
<author><name sortKey="Helt, Ga" uniqKey="Helt G">GA Helt</name>
</author>
<author><name sortKey="Blanchard, Sg" uniqKey="Blanchard S">SG Blanchard</name>
</author>
<author><name sortKey="Raja, A" uniqKey="Raja A">A Raja</name>
</author>
<author><name sortKey="Loraine, Ae" uniqKey="Loraine A">AE Loraine</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lee, E" uniqKey="Lee E">E Lee</name>
</author>
<author><name sortKey="Helt, Ga" uniqKey="Helt G">GA Helt</name>
</author>
<author><name sortKey="Reese, Jt" uniqKey="Reese J">JT Reese</name>
</author>
<author><name sortKey="Munoz Torres, Mc" uniqKey="Munoz Torres M">MC Munoz-Torres</name>
</author>
<author><name sortKey="Childers, Cp" uniqKey="Childers C">CP Childers</name>
</author>
<author><name sortKey="Buels, Rm" uniqKey="Buels R">RM Buels</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="O Onnor, Bd" uniqKey="O Onnor B">BD O’Connor</name>
</author>
<author><name sortKey="Merriman, B" uniqKey="Merriman B">B Merriman</name>
</author>
<author><name sortKey="Nelson, Sf" uniqKey="Nelson S">SF Nelson</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hilgert, U" uniqKey="Hilgert U">U Hilgert</name>
</author>
<author><name sortKey="Uwe, H" uniqKey="Uwe H">H Uwe</name>
</author>
<author><name sortKey="Sheldon, M" uniqKey="Sheldon M">M Sheldon</name>
</author>
<author><name sortKey="Mohammed, K" uniqKey="Mohammed K">K Mohammed</name>
</author>
<author><name sortKey="Jason, W" uniqKey="Jason W">W Jason</name>
</author>
<author><name sortKey="Cornel, G" uniqKey="Cornel G">G Cornel</name>
</author>
<author><name sortKey="David, M" uniqKey="David M">M David</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Campbell, Ms" uniqKey="Campbell M">MS Campbell</name>
</author>
<author><name sortKey="Holt, C" uniqKey="Holt C">C Holt</name>
</author>
<author><name sortKey="Moore, B" uniqKey="Moore B">B Moore</name>
</author>
<author><name sortKey="Yandell, M" uniqKey="Yandell M">M Yandell</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Holt, C" uniqKey="Holt C">C Holt</name>
</author>
<author><name sortKey="Yandell, M" uniqKey="Yandell M">M Yandell</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Goodstein, Dm" uniqKey="Goodstein D">DM Goodstein</name>
</author>
<author><name sortKey="Shu, S" uniqKey="Shu S">S Shu</name>
</author>
<author><name sortKey="Howson, R" uniqKey="Howson R">R Howson</name>
</author>
<author><name sortKey="Neupane, R" uniqKey="Neupane R">R Neupane</name>
</author>
<author><name sortKey="Hayes, Rd" uniqKey="Hayes R">RD Hayes</name>
</author>
<author><name sortKey="Fazo, J" uniqKey="Fazo J">J Fazo</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Krishnakumar, V" uniqKey="Krishnakumar V">V Krishnakumar</name>
</author>
<author><name sortKey="Hanlon, Mr" uniqKey="Hanlon M">MR Hanlon</name>
</author>
<author><name sortKey="Contrino, S" uniqKey="Contrino S">S Contrino</name>
</author>
<author><name sortKey="Ferlanti, Es" uniqKey="Ferlanti E">ES Ferlanti</name>
</author>
<author><name sortKey="Karamycheva, S" uniqKey="Karamycheva S">S Karamycheva</name>
</author>
<author><name sortKey="Kim, M" uniqKey="Kim M">M Kim</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Goff, Sa" uniqKey="Goff S">SA Goff</name>
</author>
<author><name sortKey="Vaughn, M" uniqKey="Vaughn M">M Vaughn</name>
</author>
<author><name sortKey="Mckay, S" uniqKey="Mckay S">S McKay</name>
</author>
<author><name sortKey="Lyons, E" uniqKey="Lyons E">E Lyons</name>
</author>
<author><name sortKey="Stapleton, Ae" uniqKey="Stapleton A">AE Stapleton</name>
</author>
<author><name sortKey="Gessler, D" uniqKey="Gessler D">D Gessler</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Fernandez Pozo, N" uniqKey="Fernandez Pozo N">N Fernandez-Pozo</name>
</author>
<author><name sortKey="Menda, N" uniqKey="Menda N">N Menda</name>
</author>
<author><name sortKey="Edwards, Jd" uniqKey="Edwards J">JD Edwards</name>
</author>
<author><name sortKey="Saha, S" uniqKey="Saha S">S Saha</name>
</author>
<author><name sortKey="Tecle, Iy" uniqKey="Tecle I">IY Tecle</name>
</author>
<author><name sortKey="Strickler, Sr" uniqKey="Strickler S">SR Strickler</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jung, S" uniqKey="Jung S">S Jung</name>
</author>
<author><name sortKey="Ficklin, Sp" uniqKey="Ficklin S">SP Ficklin</name>
</author>
<author><name sortKey="Lee, T" uniqKey="Lee T">T Lee</name>
</author>
<author><name sortKey="Cheng, C H" uniqKey="Cheng C">C-H Cheng</name>
</author>
<author><name sortKey="Blenda, A" uniqKey="Blenda A">A Blenda</name>
</author>
<author><name sortKey="Zheng, P" uniqKey="Zheng P">P Zheng</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Alexandrov, N" uniqKey="Alexandrov N">N Alexandrov</name>
</author>
<author><name sortKey="Tai, S" uniqKey="Tai S">S Tai</name>
</author>
<author><name sortKey="Wang, W" uniqKey="Wang W">W Wang</name>
</author>
<author><name sortKey="Mansueto, L" uniqKey="Mansueto L">L Mansueto</name>
</author>
<author><name sortKey="Palis, K" uniqKey="Palis K">K Palis</name>
</author>
<author><name sortKey="Fuentes, Rr" uniqKey="Fuentes R">RR Fuentes</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Harris, Tw" uniqKey="Harris T">TW Harris</name>
</author>
<author><name sortKey="Baran, J" uniqKey="Baran J">J Baran</name>
</author>
<author><name sortKey="Bieri, T" uniqKey="Bieri T">T Bieri</name>
</author>
<author><name sortKey="Cabunoc, A" uniqKey="Cabunoc A">A Cabunoc</name>
</author>
<author><name sortKey="Chan, J" uniqKey="Chan J">J Chan</name>
</author>
<author><name sortKey="Chen, Wj" uniqKey="Chen W">WJ Chen</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Shimoyama, M" uniqKey="Shimoyama M">M Shimoyama</name>
</author>
<author><name sortKey="De Pons, J" uniqKey="De Pons J">J De Pons</name>
</author>
<author><name sortKey="Hayman, Gt" uniqKey="Hayman G">GT Hayman</name>
</author>
<author><name sortKey="Laulederkind, Sjf" uniqKey="Laulederkind S">SJF Laulederkind</name>
</author>
<author><name sortKey="Liu, W" uniqKey="Liu W">W Liu</name>
</author>
<author><name sortKey="Nigam, R" uniqKey="Nigam R">R Nigam</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hammond, S" uniqKey="Hammond S">S Hammond</name>
</author>
<author><name sortKey="Kaplarevic, M" uniqKey="Kaplarevic M">M Kaplarevic</name>
</author>
<author><name sortKey="Borth, N" uniqKey="Borth N">N Borth</name>
</author>
<author><name sortKey="Betenbaugh, Mj" uniqKey="Betenbaugh M">MJ Betenbaugh</name>
</author>
<author><name sortKey="Lee, Kh" uniqKey="Lee K">KH Lee</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Poelchau, M" uniqKey="Poelchau M">M Poelchau</name>
</author>
<author><name sortKey="Childers, C" uniqKey="Childers C">C Childers</name>
</author>
<author><name sortKey="Moore, G" uniqKey="Moore G">G Moore</name>
</author>
<author><name sortKey="Tsavatapalli, V" uniqKey="Tsavatapalli V">V Tsavatapalli</name>
</author>
<author><name sortKey="Evans, J" uniqKey="Evans J">J Evans</name>
</author>
<author><name sortKey="Lee, C Y" uniqKey="Lee C">C-Y Lee</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Forbes, Sa" uniqKey="Forbes S">SA Forbes</name>
</author>
<author><name sortKey="Beare, D" uniqKey="Beare D">D Beare</name>
</author>
<author><name sortKey="Gunasekaran, P" uniqKey="Gunasekaran P">P Gunasekaran</name>
</author>
<author><name sortKey="Leung, K" uniqKey="Leung K">K Leung</name>
</author>
<author><name sortKey="Bindal, N" uniqKey="Bindal N">N Bindal</name>
</author>
<author><name sortKey="Boutselakis, H" uniqKey="Boutselakis H">H Boutselakis</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wang, L S" uniqKey="Wang L">L-S Wang</name>
</author>
<author><name sortKey="Li San, W" uniqKey="Li San W">W Li-San</name>
</author>
<author><name sortKey="Li San, W" uniqKey="Li San W">W Li-San</name>
</author>
<author><name sortKey="Otto, V" uniqKey="Otto V">V Otto</name>
</author>
<author><name sortKey="Childress, Dm" uniqKey="Childress D">DM Childress</name>
</author>
<author><name sortKey="Amanda, P" uniqKey="Amanda P">P Amanda</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Wattam, Ar" uniqKey="Wattam A">AR Wattam</name>
</author>
<author><name sortKey="Abraham, D" uniqKey="Abraham D">D Abraham</name>
</author>
<author><name sortKey="Dalay, O" uniqKey="Dalay O">O Dalay</name>
</author>
<author><name sortKey="Disz, Tl" uniqKey="Disz T">TL Disz</name>
</author>
<author><name sortKey="Driscoll, T" uniqKey="Driscoll T">T Driscoll</name>
</author>
<author><name sortKey="Gabbard, Jl" uniqKey="Gabbard J">JL Gabbard</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Mungall, Cj" uniqKey="Mungall C">CJ Mungall</name>
</author>
<author><name sortKey="Emmert, Db" uniqKey="Emmert D">DB Emmert</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Roy, S" uniqKey="Roy S">S Roy</name>
</author>
<author><name sortKey="Ernst, J" uniqKey="Ernst J">J Ernst</name>
</author>
<author><name sortKey="Kharchenko, Pv" uniqKey="Kharchenko P">PV Kharchenko</name>
</author>
<author><name sortKey="Kheradpour, P" uniqKey="Kheradpour P">P Kheradpour</name>
</author>
<author><name sortKey="Negre, N" uniqKey="Negre N">N Negre</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gerstein, Mb" uniqKey="Gerstein M">MB Gerstein</name>
</author>
<author><name sortKey="Lu, Zj" uniqKey="Lu Z">ZJ Lu</name>
</author>
<author><name sortKey="Van Nostrand, El" uniqKey="Van Nostrand E">EL Van Nostrand</name>
</author>
<author><name sortKey="Cheng, C" uniqKey="Cheng C">C Cheng</name>
</author>
<author><name sortKey="Arshinoff, Bi" uniqKey="Arshinoff B">BI Arshinoff</name>
</author>
<author><name sortKey="Liu, T" uniqKey="Liu T">T Liu</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Li, H" uniqKey="Li H">H Li</name>
</author>
<author><name sortKey="Handsaker, B" uniqKey="Handsaker B">B Handsaker</name>
</author>
<author><name sortKey="Wysoker, A" uniqKey="Wysoker A">A Wysoker</name>
</author>
<author><name sortKey="Fennell, T" 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>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Biol</journal-id>
<journal-id journal-id-type="iso-abbrev">Genome Biol</journal-id>
<journal-title-group><journal-title>Genome Biology</journal-title>
</journal-title-group>
<issn pub-type="ppub">1474-7596</issn>
<issn pub-type="epub">1474-760X</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
<publisher-loc>London</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">27072794</article-id>
<article-id pub-id-type="pmc">4830012</article-id>
<article-id pub-id-type="publisher-id">924</article-id>
<article-id pub-id-type="doi">10.1186/s13059-016-0924-1</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Software</subject>
</subj-group>
</article-categories>
<title-group><article-title>JBrowse: a dynamic web platform for genome visualization and analysis</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Buels</surname>
<given-names>Robert</given-names>
</name>
<address><email>rbuels@gmail.com</email>
</address>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Yao</surname>
<given-names>Eric</given-names>
</name>
<address><email>ericiam@berkeley.edu</email>
</address>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Diesh</surname>
<given-names>Colin M.</given-names>
</name>
<address><email>dieshc@missouri.edu</email>
</address>
<xref ref-type="aff" rid="Aff2"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hayes</surname>
<given-names>Richard D.</given-names>
</name>
<address><email>rdhayes@lbl.gov</email>
</address>
<xref ref-type="aff" rid="Aff3"></xref>
<xref ref-type="aff" rid="Aff6"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Munoz-Torres</surname>
<given-names>Monica</given-names>
</name>
<address><email>mcmunozt@lbl.gov</email>
</address>
<xref ref-type="aff" rid="Aff3"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Helt</surname>
<given-names>Gregg</given-names>
</name>
<address><email>gregghelt@gmail.com</email>
</address>
<xref ref-type="aff" rid="Aff3"></xref>
<xref ref-type="aff" rid="Aff4"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Goodstein</surname>
<given-names>David M.</given-names>
</name>
<address><email>dmgoodstein@lbl.gov</email>
</address>
<xref ref-type="aff" rid="Aff3"></xref>
<xref ref-type="aff" rid="Aff6"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Elsik</surname>
<given-names>Christine G.</given-names>
</name>
<address><email>chris.elsik@gmail.com</email>
</address>
<xref ref-type="aff" rid="Aff2"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lewis</surname>
<given-names>Suzanna E.</given-names>
</name>
<address><email>selewis@lbl.gov</email>
</address>
<xref ref-type="aff" rid="Aff3"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Stein</surname>
<given-names>Lincoln</given-names>
</name>
<address><email>lincoln.stein@gmail.com</email>
</address>
<xref ref-type="aff" rid="Aff5"></xref>
<xref ref-type="aff" rid="Aff7"></xref>
</contrib>
<contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0001-7639-5369</contrib-id>
<name><surname>Holmes</surname>
<given-names>Ian H.</given-names>
</name>
<address><email>ihholmes@gmail.com</email>
</address>
<xref ref-type="aff" rid="Aff1"></xref>
<xref ref-type="aff" rid="Aff3"></xref>
</contrib>
<aff id="Aff1"><label></label>
Department of Bioengineering, University of California, Berkeley, California USA</aff>
<aff id="Aff2"><label></label>
Division of Animal Sciences, University of Missouri, Columbia, Missouri USA</aff>
<aff id="Aff3"><label></label>
Lawrence Berkeley National Laboratory, Berkeley, California USA</aff>
<aff id="Aff4"><label></label>
Current affiliation: Genomancer Consulting, Healdsburg, California USA</aff>
<aff id="Aff5"><label></label>
Ontario Institute of Cancer Research, Toronto, Ontario Canada</aff>
<aff id="Aff6"><label></label>
US Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA</aff>
<aff id="Aff7"><label></label>
Department of Molecular Genetics, University of Toronto, Toronto, Ontario Canada</aff>
</contrib-group>
<pub-date pub-type="epub"><day>12</day>
<month>4</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>12</day>
<month>4</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="collection"><year>2016</year>
</pub-date>
<volume>17</volume>
<elocation-id>66</elocation-id>
<history><date date-type="received"><day>4</day>
<month>1</month>
<year>2016</year>
</date>
<date date-type="accepted"><day>15</day>
<month>3</month>
<year>2016</year>
</date>
</history>
<permissions><copyright-statement>© Buels et al. 2016</copyright-statement>
<license license-type="OpenAccess"><license-p><bold>Open Access</bold>
This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>
) applies to the data made available in this article, unless otherwise stated.</license-p>
</license>
</permissions>
<abstract id="Abs1"><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>
</abstract>
<kwd-group xml:lang="en"><title>Keywords</title>
<kwd>Genome</kwd>
<kwd>Browser</kwd>
<kwd>Bioinformatics</kwd>
</kwd-group>
<funding-group><award-group><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000051</institution-id>
<institution>National Human Genome Research Institute</institution>
</institution-wrap>
</funding-source>
<award-id>HG004483</award-id>
<principal-award-recipient><name><surname>Holmes</surname>
<given-names>Ian H.</given-names>
</name>
</principal-award-recipient>
</award-group>
<award-group><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000057</institution-id>
<institution>National Institute of General Medical Sciences</institution>
</institution-wrap>
</funding-source>
<award-id>GM080203</award-id>
<principal-award-recipient><name><surname>Lewis</surname>
<given-names>Suzanna E.</given-names>
</name>
</principal-award-recipient>
</award-group>
</funding-group>
<custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name>
<meta-value>© The Author(s) 2016</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
</front>
</pmc>
<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>
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