Setting Up the JBrowse Genome Browser
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- Abstract
- Table of Contents
- Figures
- Literature Cited
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
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
Materials
Figures
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Figure 9.13.1 JBrowse instance with just DNA sequence track, zoomed in to the individual base level. View Image -
Figure 9.13.2 Screenshot of JBrowse with newly created “gene” track. View Image -
Figure 9.13.3 Screenshot of JBrowse instance with newly created “remark” track. View Image -
Figure 9.13.4 Screenshot of JBrowse instance with newly created quantitative track. View Image
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. |
