Setting Up the JBrowse Genome Browser

Mitchell E. Skinner1, Ian H. Holmes1

1 University of California at Berkeley, Berkeley, California
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 9.13
DOI:  10.1002/0471250953.bi0913s32
Online Posting Date:  December, 2010
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Abstract

JBrowse is a Web‐based tool for visualizing genomic data. Unlike most other Web‐base genome browsers, JBrowse exploits the capabilities of the user's Web browser to make scrolling and zooming fast and smooth. It supports the browsers used by almost all Internet users, and is relatively simple to install. JBrowse can utilize multiple types of data in a variety of common genomic data formats, including genomic feature data in bioperl databases, GFF files, BED files, and quantitative data in wiggle files. This unit describes how to obtain the JBrowse software, set it up on a Linux or Mac OS X computer running as a Web server, and incorporate genome annotation data from multiple sources into JBrowse. After completing the protocols described in this unit, the reader will have a Web site that other users can visit to browse the genomic data. Curr. Protoc. Bioinform. 32:9.13.1‐9.13.13. © 2010 by John Wiley & Sons, Inc.

Keywords: genome browser; visualization; JBrowse; gff; bed; wiggle; GenBank

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Setting Up a JBrowse Instance Using Flatfiles as a Data Source
  • Alternate Protocol 1: Setting Up a JBrowse Instance Using a Relational Database as the Data Source
  • Alternate Protocol 2: Setting Up a JBrowse Instance Using NCBI GenBank Files as a Data Source
  • Support Protocol 1: Downloading/Installing JBrowse
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

   Hubbard, T.J., Aken, B.L., Beal, K., Ballester, B., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cunningham, F., Cutts, T., Down, T., Dyer, S.C., Fitzgerald, S., Fernandez‐Banet, J., Graf, S., Haider, S., Hammond, M., Herrero, J., Holland, R., Howe, K., Howe, K., Johnson, N., Kahari, A., Keefe, D., Kokocinski, F., Kulesha, E., Lawson, D., Longden, I., Melsopp, C., Megy, K., Meidl, P., Ouverdin, B., Parker, A., Prlic, A., Rice, S., Rios, D., Schuster, M., Sealy, I., Severin, J., Slater, G., Smedley, D., Spudich, G., Trevanion, S., Vilella, A., Vogel, J., White, S., Wood, M., Cox, T., Curwen, V., Durbin, R., Fernandez‐Suarez, X.M., Flicek, P., Kasprzyk, A., Proctor, G., Searle, S., Smith, J., Ureta‐Vidal, A., and Birney, E. 2007. Ensembl 2007. Nucleic Acids Res. 35:D610‐D617.
   Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M., and Haussler, D. 2002. The human genome browser at UCSC. Genome Res. 12:996‐1006.
   Skinner, M.E., Uzilov, A.V., Stein, L.D., Mungall, C.J., and Holmes, I.H. 2009. JBrowse: A next‐generation genome browser. Genome Res. 19:1630‐1638.
   Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A., and Lewis, S. 2002. The generic genome browser: A building block for a model organism system database. Genome Res. 12:1599‐1610.
Key Reference
   Skinner et al., 2009. See above.
  This article describes in detail how JBrowse works.
Internet Resources
  http://jbrowse.org/
  The main JBrowse Web site: has links to the JBrowse code, documentation, email lists, publications, and other Internet resources relevant to JBrowse.
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