Introduction

The Integrated Genome Browser (IGB, pronounced Ig-Bee) provides advanced, highly-customizable environment for exploring and analyzing genomic data sets.  Using IGB, you can:

• View your RNA-Seq, ChIP-chip or ChIP-seq data alongside publicly-available genome annotations and sequence.
• Visualize and compare multiple genomic annotations data sets from a variety of public and private sources.
• Investigate questions related to alternative splicing, regulation of gene expression, epigenetic modifications of DNA, and many others.
• View results from aligning short-read sequences onto a target genome, identify SNPs, and check alignment quality.
• Copy segments of genomic data for further analysis in other tools, such as primer design tools.
• Create high-quality images for publication in a variety of formats, including PDF, PNG, and more.

If you use IGB in your research, please cite this article:

Nicol JW, Helt GA, Blanchard SG Jr, Raja A, Loraine AE.

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.
Bioinformatics. 2009 Oct 15;25(20):2730-1. Epub 2009 Aug 4. PubMed PMID:

19654113; PubMed Central PMCID: PMC2759552.http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2759552/?tool=pubmed

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2759552

IGB unique features and benefits

IGB lets you view results from your own experiments or computational analyses alongside public domain gene annotations, sequence, and genomic data sets, thus making it easier for you to determine how your experiments disagree or agree with current thinking and models of genomic structure.

Some of the features IGB offers include:

• Draggable graphs. You can display genome graphs data (e.g., "bar" and "wig" files) alongside and even on top of reference genome annotations, thus making it easier to see how your experimental results match up to the published reference genome annotations.
• Integration with local and remote external data sources. IGB can load data from a variety of sources, including Distributed Annotation Servers, Quickload servers, ordinary Web sites, and local files.
• Intron-trimming sliced view. In many species, introns are huge when compared to the exonic (coding) regions of genes. IGB provides a Sliced View tab that trims uninformative regions of introns.
• Web-controls. IGB can be controlled from a web browser or any other program capable of sending HTTP requests. Via IGB links, you can create Web pages that direct IGB to scroll to a specific region and load data sets from local files or servers.
• Open source. All development on IGB proceeds via a 100% open source model. The license allows developers to incorporate IGB (and its components) into new applications.