Scientists at the University of Maryland have developed a new, web-based tool that enables researchers to quickly and easily visualize and compare large amounts of genomic information resulting from high-throughput sequencing experiments. The free tool, called Epiviz, was described in a paper published online on August 3, 2014 in the journal Nature Methods.
Next-generation sequencing has revolutionized functional genomics. These techniques are key to understanding the molecular mechanisms underlying cell function in healthy and diseased individuals and the development of diseases like cancer. Data from multiple experiments need to be integrated, but the growing number of data sets makes a thorough comparison and analysis of results challenging.
To visualize and browse entire genomes, graphical interfaces that display information from a database of genomic datacalled "genome browsers"were created. Epiviz offers a major advantage over browsers currently available: Epiviz seamlessly integrates with the open-source Bioconductor analysis software widely used by genomic scientists, through its Epivizr Bioconductor package.
"Prior tools limited visualization to presentation and dissemination, rather than a hybrid tool integrating interactive visualization with algorithmic analysis," says Hctor Corrada Bravo, assistant professor in computer science at UMD. He also has an appointment in the Center for Bioinformatics and Computational Biology of the university's Institute for Advanced Computer Studies.
Because Epiviz is based on the Bioconductor infrastructure, the tool supports many popular next-generation sequencing techniques, such as ChIP-seq, which is used to analyze protein interactions with DNA; RNA-seq, which reveals a comprehensive snapshot of the abundance of RNAs in cells; and DNA methylation analyses.
Epiviz implements multiple visualization methods for location-based data (such as genomic regions of in
|Contact: Abby Robinson|
University of Maryland