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
Bitbucket
Bitbucket is a Git-based source code repository hosting service owned by Atlassian. Bitbucket offers both commercial plans and free accounts with an unlimited number of private repositories.
Services Bitbucket Cloud
Bitbucket Cloud (previ ...
.
Description
IGB is built on top of the Genoviz SDK,
a
Java
Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's mos ...
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
Rest or REST may refer to:
Relief from activity
* Sleep
** Bed rest
* Kneeling
* Lying (position)
* Sitting
* Squatting position
Structural support
* Structural support
** Rest (cue sports)
** Armrest
** Headrest
** Footrest
Arts and enter ...
-style Web services (
Distributed Annotation System Distribution may refer to:
Mathematics
*Distribution (mathematics), generalized functions used to formulate solutions of partial differential equations
* Probability distribution, the probability of a particular value or value range of a vari ...
) and a simple file-system based approach called QuickLoad.
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
{{reflist
External links
Genoviz SDK at BitbucketIGB installer download site
Free bioinformatics software