Software tool helps visualize genomes


The Broad Institute of MIT and Harvard has created and released for free a software browser to help researchers better visualize and manipulate entire genomes.

"Currently available browsers did not meet the visualization needs of people who work with sequence data every day, especially those people doing manual annotation," said David DeCaprio, leader of the Broad's annotation team.

Enter the new software, dubbed Argo. "Other browsers aren't as easy to use, or as powerful at visualization. We wanted to set a new standard," DeCaprio said.

Many regions of the genome have been identified as interesting. "The problem is, programs have identified so many overlapping regions of interest, it's difficult for biologists to make sense of them by just looking at the coordinates," said Reinhard Engels, a software engineer at the Broad.

Argo helps users "read" the genome because the places where working sequences stop and start are flagged, and it contains footnotes on what the sequence may be responsible for in the organism. "It's like having an annotated version of Shakespeare where you see not just one interpretation of a quote, but all the prominent scholars' comments," Engels said.

Because Argo displays genomic data with a spatial perspective that makes it easy to appreciate the overall structure of the gene, it could help teach students the basics of gene structure and how the outputs of various kinds of genome-analysis software differ from one another, its developers said.

Argo also improves data access by making it easier to automatically retrieve data from genomic websites and to load in data directly from the results produced by popular analysis programs.

The browser is already getting positive feedback from scientists who've used it. "Argo provides an extremely intuitive, user-friendly, and versatile platform for the visualization and manipulation of complex features across a genome. Its ease of use greatly facilitates the process of genomic investigation for the regular biologist," said Patrick Tan, a researcher at Singapore's National Cancer Center and the Genome Institute in Singapore.

Said Professor Matthew Sachs of Oregon Health and Science University, "Importantly, Argo's developers are providing this tool freely to the academic community and are responsive to the needs of its users."

Additional members of the Argo team include Sarah Calvo, Mark Borowsky, Tim Elkins, Chinnappa Kodira, Randy Milbert, Sinead O'Leary, Seth Purcell, Shunguang Wang, Charlie Whittaker, Yuhong Wu, James Galagan and Jill Mesirov.

The Broad Institute is known officially as the Eli and Edythe L. Broad Institute. It is a research collaboration of MIT, Harvard University and its hospitals, and the Whitehead Institute for Biomedical Research.

Argo is available for download at http://www.broad.mit.edu/annotation/argo.


Topics: Bioengineering and biotechnology, Genetics

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