What is it?

The genome browser is software tool for visualizing of high-density data plotted against coordinates on the genome. Tiling arrays, ChIP-chip, and high-throughput sequencing are a few potential uses. The genome browser is designed to gracefully handle large datasets, allow easy import of user data, and interoperates with other bioinformatics tools through the Gaggle framework.

more screenshots

Launch the genome browser

Launch empty genome browser.

Demos

Finding protein-DNA binding sites with MeDiChI.

Launch demo genome browser with Halobacterium salinarum tiling array and ChIP-chip data.

Other web start packages containing prepackaged data from H. salinarum can be found on the Halo Gaggle page.

Bacillus anthracis RNA-seq data from Structure and complexity of a bacterial transcriptome.

DNA binding locations of CTCF and STAG1 in Human.

Features

• Interactively pan and zoom across whole genome
• Import genome from UCSC genome browser
• Import genome from local files
• Import data in GFF format
• Render data tracks in several formats: scaling bubble plot, heatmap, segmentation, lines, markers, and bars.
• Bookmark and annotate interesting regions and features
• Link out to UCSC genome browser
• Embedded Sqlite database
  • responsive UI for large datasets
  • ability to handle tracks that don't fit into memory
  • eases importing tracks and building datasets
  • smaller memory footprint

Documentation

Help is available on several aspects of the genome browser:

• getting started
• creating a new project
• importing data into the genome browser
• exchanging data with other tools through the gaggle
• R interoperability

The wiki provides more information. For developers, see the design and architecture overview or javadocs.

Support

For questions and support contact the Gaggle mailing lists.

Bugs / Feature requests

Please submit bugs and feature requests to our issue tracker. Anyone can create an account.

Source

Source code is available from our subversion repository. Please contact us to submit patches or contribute code.

http://gaggle.systemsbiology.net/svn/gaggle/genomebrowser/

Citation

This software was developed in the Baliga Lab at the Institute for Systems Biology.