Introduction

Next-generation sequencing technologies are making it much easier for labs to produce huge volumes of short- and long-read sequencing data. More mature genome-scale technologies, such as tiling arrays, continue to be used in many labs to interrogate expression patterns, identify sites bound by transcriptional factors, and explore the epigenome.  To understand what these new data sets mean, researchers need to view their data alongside other known features of the genomic landscape.

The Integrated Genome Browser (IGB, pronounced Ig-Bee) aims to meet this need. First developed at Affymetrix in 2003 for their tiling array products, IGB provides advanced, highly-customizable environment for exploring and analyzing large-scale genomic data sets.

Using IGB, you can:

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

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:

• Animated zooming. Most genome browsers implement "jump zooming," in which you click a zoom button (or other type of control) and then wait for the display to re-draw. In IGB, zooming is animated, allowing you to easily and quickly adjust the zoom level as needed.
• 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.
• Edge-matching across tracks. When you click an item in the display, anything else in the same or different tracks that have identical boundaries lights up, highlighting interesting similarities or differences across gene models, sequence reads, or other features.
• 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 from 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.