Gambit
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Application data |
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| Principal bioinformatics method(s) | Visualisation |
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| Created at | The Marth Lab |
| Maintained? | Yes |
| Licence | GPL 2.0+, Commercial |
Summary: A cross-platform GUI for sequence visualization and analysis.
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Gambit is a new cross-platform GUI (graphical user interface) application for sequence visualization and analysis.
Our software takes advantage of the indexing features of the (fairly) recently standardized BAM sequence alignment format that allows rapid access to genomic data, with minimal startup time and re-rendering delay. Gambit also supports a variety of annotation formats (BED, GFF, GFF3, VCF) "out-of-the-box" for displaying gene/region annotations as well as SNP entries.
Gambit is currently "plugin-aware" with respect to format support, meaning support for new formats can be added without needing to modify/upgrade the main program itself.
Bioinformatics analysis of sequence data currently requires specialized expertise and is rapidly becoming a bottleneck. Analysis needs of smaller biology laboratories can be served if the visualization software integrates essential analytical functionality. Such functionality includes PCR primer design to support candidate SNP validation experiments; connecting to common databases; exporting data from specific regions of the chromosome for detailed and focused analysis.
Gambit will soon be "plugin-aware" with respect to analytical tools to provide such integrated functions. One benefit from implementing the analysis system via plugins is that anyone with programming skills can readily include their own custom features: support for new file formats, additional metrics, or even custom views. Another benefit is that users need not add every plugin. You will be able customize Gambit to be as lightweight or fully-functional as your needs require.
AVAILABILITY:
Contents
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Grab the latest copy of our tools on the Marth lab web page:
http://bioinformatics.bc.edu/marthlab/Mosaik http://bioinformatics.bc.edu/marthlab/Gambit
By popular demand, MOSAIK and Gambit now dual licensed under the GPL 2.0+ and via a commercial license available from the Marth Lab. The source code is available on our Google Code sites:
http://code.google.com/p/mosaik-aligner http://code.google.com/p/gambit-viewer
BUG REPORTS:
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Please report bugs only through our bug report websites:
http://code.google.com/p/mosaik-aligner/issues/list http://code.google.com/p/gambit-viewer/issues/list
Thank you for using our software. We hope you find these tools useful in your research.
Links
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References
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