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. 2010 Dec:Chapter 9:Unit 9.13.
doi: 10.1002/0471250953.bi0913s32.

Setting up the JBrowse genome browser

Mitchell E Skinner  1 , Ian H Holmes
Affiliations

Setting up the JBrowse genome browser

Mitchell E Skinner et al. Curr Protoc Bioinformatics. 2010 Dec.

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.

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Figures

Figure A.1B.1
Figure A.1B.1
A sample FASTA file that contains the sequences for two homologous proteins, actophorin and yeast cofilin. Note that a greater-than sign (>) designates the beginning of each entry and that each of the lines of sequence contains less than 80 characters.
Figure A.1B.2
Figure A.1B.2
A sample GenBank record. Circled numbers identify the fields listed in Table A.1B.1.
Figure A.1B.3
Figure A.1B.3
A sample PHYLIP-formatted file. The five sequences shown are HIV-1 and HIV-2 gag proteins from a variety of isolates. See text for details.
Figure A.1B.4
Figure A.1B.4
A sample MSF-formatted file. The five sequences shown are HIV-1 and HIV-2 gag proteins from a variety of isolates. See text for details.
Figure A.1B.5
Figure A.1B.5
A sample Nexus-formatted file. The five sequences shown are HIV-1 and HIV-2 gag proteins from a variety of isolates. See text for details.
Figure 9.13.1
Figure 9.13.1
JBrowse instance with just DNA sequence track, zoomed in to the individual base level.
Figure 9.13.2
Figure 9.13.2
Screenshot of JBrowse with newly-created “gene” track.
Figure 9.13.3
Figure 9.13.3
Screenshot of JBrowse instance with newly-created “Remark” track.
Figure 9.13.4
Figure 9.13.4
Screenshot of JBrowse instance with newly-created quantitative track.
See this image and copyright information in PMC

References

Literature Cited

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Key Reference

    1. Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH. JBrowse: A next-generation genome browser. Genome Res. 2009;19:1630–8. - PMC - PubMed

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