Visualizing genomes

IGB-start-screenThanks to always improving DNA sequencing technologies, biologists now have access to the full genome sequences for dozens of plants and animals. In addition, many individuals now have access to their own personal genome sequences.  To understand all this, we need user-friendly software that translates esoteric strings of DNA letters into interactive images we can easily explore and understand.

loraineLab-visualizingGenomes-2To meet this need, we developed Integrated Genome Browser (IGB), a fast, flexible, and free graphical user interface for visualizing and understanding genome sequence data.

IGB is a desktop software program you download from our Web site and run on your local computer. Once downloaded, IGB lets you connect to reference genome sequence data from many species. And you can also load your own data from your desktop computer.

IGB implements innovative but practical visualization techniques that stimulate creativity and insight.  Unlike much slower and clunkier genome browser tools, IGB implements genome-scale, animated zooming. This lets you zoom from chromosome to base pair and back again in a single sweep of the mouse. IGB also focuses zooming on the location of your last click, which helps you keep track of where you’ve been and where you’re going. Animated zooming in IGB makes moving around your genomic data feel like flying.

FixedTrackHeightIGB also offers many options for building sophisticated, attractive, and informative data visualizations, a feature that is especially important for scientists and educators. IGB lets you fine-tune size and resolution of images, making it easy to produce high-quality images.

Using the IGB Annotation tab, you can configure colors, add or remove arrows indicating whether a gene or read is on the minus or plus strand, add or remove labels, fine-tune track heights, and perform operations on tracks.

You can even filter tracks so that only certain types of data are shown, such as sequence reads that contain introns – or don’t. You can also hide, show, or color-code annotations based on their score, which can be especially useful when sifting through quantitative data such as ChIP-Seq peaks. In the image above, we configured IGB to use yellow and magenta for plus and minus strand RNA-Seq reads. We also locked the height of the gene models track.

IGB already has dozens of features, but often scientists need to build specialized visualizations unique to their data or particular research questions. Scientists are constantly thinking of new questions, and there is no way anyone could ever predict every feature scientists will need! For this reason, we designed IGB to be easy-to-modify and easy-to-extend. Our idea is that developers working closely with scientists can add new functionality to IGB as plug-ins called IGB Apps. Developers distribute their Apps to the community using the IGB App Store.