Integrated Genome Browser (IGB) (pronounced Ig-Bee) is an open-source

genome browser In bioinformatics, a genome browser is a graphical interface for display of information from a biological database Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughp ...

, a

visualization Visualization or visualisation may refer to: * Visualization (graphics), the physical or imagining creation of images, diagrams, or animations to communicate a message * Data visualization, the graphic representation of data * Information visuali ...

tool used to observe biologically-interesting patterns in genomic data sets, including sequence data, gene models, alignments, and data from

DNA microarrays A DNA microarray (also commonly known as DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to g ...

History

Integrated Genome Browser was first developed at Affymetrix for their scientists and public sector collaborators to visualize data from genome-wide tiling arrays. The first iterations of IGB were developed using funding from

NIH The National Institutes of Health, commonly referred to as NIH (with each letter pronounced individually), is the primary agency of the United States government responsible for biomedical and public health research. It was founded in the late ...

awarded to company scientists Gregg Helt and Tom Gingeras. In 2004, Affymetrix released IGB as open source software, along with the Genoviz SDK, a graphics library for building genome browser applications. The first release of the code base was done as a compressed file archive. Soon after, the code was imported into a new repository at SourceForge. Since then, all development has proceeded in public under an open source model. In early 2008, a group led by former Affymetrix employee Ann Loraine began developing and maintaining IGB, supported by funding from the National Science Foundation and new investigator funds from UNC Charlotte. Since then, Loraine, her students, and collaborators have added many new features and capabilities, notably support for visualizing high-throughput sequencing data from Illumina and other platforms. In 2014, they migrated the source code to a git repository at

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Description

IGB is built on top of the Genoviz SDK, a

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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

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-style Web services (

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) and a simple file-system based approach called QuickLoad. Integrated Genome Browser 9

Supported formats

IGB reads data in dozens of formats, including BAM, BED, Affymetrix CHP,

FASTA FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics. History The original FASTA program ...

, 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

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External links

Genoviz SDK at Bitbucket

IGB installer download site
Free bioinformatics software