JBrowse: a dynamic web platform for genome visualization and analysis

BACKGROUND: 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. RESULTS: Overall improvements to speed and scalability are accompanied by specific enhancements that support co...

Descripción completa

Detalles Bibliográficos
Autores principales: Buels, Robert, Yao, Eric, Diesh, Colin M., Hayes, Richard D., Munoz-Torres, Monica, Helt, Gregg, Goodstein, David M., Elsik, Christine G., Lewis, Suzanna E., Stein, Lincoln, Holmes, Ian H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4830012/
https://www.ncbi.nlm.nih.gov/pubmed/27072794
http://dx.doi.org/10.1186/s13059-016-0924-1
_version_ 1782426839929585664
author Buels, Robert
Yao, Eric
Diesh, Colin M.
Hayes, Richard D.
Munoz-Torres, Monica
Helt, Gregg
Goodstein, David M.
Elsik, Christine G.
Lewis, Suzanna E.
Stein, Lincoln
Holmes, Ian H.
author_facet Buels, Robert
Yao, Eric
Diesh, Colin M.
Hayes, Richard D.
Munoz-Torres, Monica
Helt, Gregg
Goodstein, David M.
Elsik, Christine G.
Lewis, Suzanna E.
Stein, Lincoln
Holmes, Ian H.
author_sort Buels, Robert
collection PubMed
description BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: JBrowse is a mature web application suitable for genome visualization and analysis.
format Online
Article
Text
id pubmed-4830012
institution National Center for Biotechnology Information
language English
publishDate 2016
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-48300122016-04-14 JBrowse: a dynamic web platform for genome visualization and analysis Buels, Robert Yao, Eric Diesh, Colin M. Hayes, Richard D. Munoz-Torres, Monica Helt, Gregg Goodstein, David M. Elsik, Christine G. Lewis, Suzanna E. Stein, Lincoln Holmes, Ian H. Genome Biol Software BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: JBrowse is a mature web application suitable for genome visualization and analysis. BioMed Central 2016-04-12 /pmc/articles/PMC4830012/ /pubmed/27072794 http://dx.doi.org/10.1186/s13059-016-0924-1 Text en © Buels et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), 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 (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Buels, Robert
Yao, Eric
Diesh, Colin M.
Hayes, Richard D.
Munoz-Torres, Monica
Helt, Gregg
Goodstein, David M.
Elsik, Christine G.
Lewis, Suzanna E.
Stein, Lincoln
Holmes, Ian H.
JBrowse: a dynamic web platform for genome visualization and analysis
title JBrowse: a dynamic web platform for genome visualization and analysis
title_full JBrowse: a dynamic web platform for genome visualization and analysis
title_fullStr JBrowse: a dynamic web platform for genome visualization and analysis
title_full_unstemmed JBrowse: a dynamic web platform for genome visualization and analysis
title_short JBrowse: a dynamic web platform for genome visualization and analysis
title_sort jbrowse: a dynamic web platform for genome visualization and analysis
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4830012/
https://www.ncbi.nlm.nih.gov/pubmed/27072794
http://dx.doi.org/10.1186/s13059-016-0924-1
work_keys_str_mv AT buelsrobert jbrowseadynamicwebplatformforgenomevisualizationandanalysis
AT yaoeric jbrowseadynamicwebplatformforgenomevisualizationandanalysis
AT dieshcolinm jbrowseadynamicwebplatformforgenomevisualizationandanalysis
AT hayesrichardd jbrowseadynamicwebplatformforgenomevisualizationandanalysis
AT munoztorresmonica jbrowseadynamicwebplatformforgenomevisualizationandanalysis
AT heltgregg jbrowseadynamicwebplatformforgenomevisualizationandanalysis
AT goodsteindavidm jbrowseadynamicwebplatformforgenomevisualizationandanalysis
AT elsikchristineg jbrowseadynamicwebplatformforgenomevisualizationandanalysis
AT lewissuzannae jbrowseadynamicwebplatformforgenomevisualizationandanalysis
AT steinlincoln jbrowseadynamicwebplatformforgenomevisualizationandanalysis
AT holmesianh jbrowseadynamicwebplatformforgenomevisualizationandanalysis

Ejemplares similares