Integrated Genome Browser
| File:Integrated Genome Browser logo.gif | |
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| Operating system | UNIX, Linux, Mac, MS-Windows |
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| Type | Bioinformatics tool |
| License | CPL 1.0 |
| Website | http://igb.bioviz.org |
Integrated Genome Browser (IGB) (pronounced Ig-Bee)[1] is an open source genome browser, a visualization tool used to observe biologically-interesting patterns in genomic data sets, including sequence data, gene models, alignments, and data from DNA microarrays.
History
Integrated Genome Browser was originally developed at Affymetrix to support visualization of data from the company's tiling array platform and was also partly supported via NIH funding. It was released as open source in 2004. The National Science Foundation later funded further development of the tool as the front end for a companion data repository for plant genomic data sets.
Description
IGB is built on top of the Genoviz SDK,[2] a Java library that implements key visualization features such as dynamic, real-time zooming and scrolling through a genomic map, a feature of the IGB browser that sets it apart from many similar tools.
IGB is also distinguished by the ease with which individual labs can set up data source servers to share data, notably, via REST-style Web services (Distributed Annotation System) and a simple file-system based approach called QuickLoad.
Supported formats
IGB reads data in dozens of formats, including BAM, BED, Affymetrix CHP, FASTA, GFF, GTF, PSL, SGR, and WIG. The most up-to-date list is available at the BioViz Wiki.
IGB can output visualized data in dozens of formats via the FreeHEP library. These include EPS, PostScript, PDF, EMF, SVG, SWF, CGM, GIF, PNG, and PPM.
References
- ^ Nicol JW, Helt GA, Blanchard SG, Raja A, Loraine AE (October 2009). "The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets". Bioinformatics. 25 (20): 2730–1. doi:10.1093/bioinformatics/btp472. PMC 2759552. PMID 19654113.
- ^ Helt GA, Nicol JW, Erwin E, et al. (25 August 2009). "Genoviz Software Development Kit: Java tool kit for building genomics visualization applications". BMC Bioinformatics. 10: 266. doi:10.1186/1471-2105-10-266. PMC 2746221. PMID 19706180.
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