Unit

UNIT 9.13 Setting Up the JBrowse Genome Browser

  1. Mitchell E. Skinner,
  2. Ian H. Holmes

Published Online: 1 DEC 2010

DOI: 10.1002/0471250953.bi0913s32

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Skinner, M. E. and Holmes, I. H. 2010. Setting Up the JBrowse Genome Browser. Current Protocols in Bioinformatics. 32:9.13:9.13.1–9.13.13.

Author Information

  1. University of California at Berkeley, Berkeley, California

Publication History

  1. Published Online: 1 DEC 2010
  2. Published Print: DEC 2010

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