Featured Research

from universities, journals, and other organizations

Software Tool Helps Visualize Genomes

Date:
January 3, 2005
Source:
Massachusetts Institute Of Technology
Summary:
The Broad Institute of MIT and Harvard have created and released for free a software browser to help researchers better visualize and manipulate entire genomes.

The Argo Genome Browser is the Broad Institute's production tool for visualizing and manually annotating whole genomes.
Credit: Image courtesy of the Broad Institute / Massachusetts Institute Of Technology

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

Related Articles


"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.


Story Source:

The above story is based on materials provided by Massachusetts Institute Of Technology. Note: Materials may be edited for content and length.


Cite This Page:

Massachusetts Institute Of Technology. "Software Tool Helps Visualize Genomes." ScienceDaily. ScienceDaily, 3 January 2005. <www.sciencedaily.com/releases/2004/12/041219165326.htm>.
Massachusetts Institute Of Technology. (2005, January 3). Software Tool Helps Visualize Genomes. ScienceDaily. Retrieved October 31, 2014 from www.sciencedaily.com/releases/2004/12/041219165326.htm
Massachusetts Institute Of Technology. "Software Tool Helps Visualize Genomes." ScienceDaily. www.sciencedaily.com/releases/2004/12/041219165326.htm (accessed October 31, 2014).

Share This



More Computers & Math News

Friday, October 31, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Protests Stall Hungary's Internet Tax

Protests Stall Hungary's Internet Tax

Reuters - Business Video Online (Oct. 31, 2014) Hungary will shelve plans to introduce a tax on internet data traffic that has generated big protests over the past week. But as Amy Pollock reports the controversial issue hasn’t gone away entirely. Video provided by Reuters
Powered by NewsLook.com
Samsung's Incredible Shrinking Smartphone Profits

Samsung's Incredible Shrinking Smartphone Profits

Reuters - Business Video Online (Oct. 30, 2014) The world's top mobile maker is under severe pressure, delivering a 60 percent drop in Q3 profit as its handset business struggles. Turning it around may not prove easy, says Reuters' Jon Gordon. Video provided by Reuters
Powered by NewsLook.com
Ban On Wearable Cameras In Movie Theaters Surprises No One

Ban On Wearable Cameras In Movie Theaters Surprises No One

Newsy (Oct. 30, 2014) The Motion Picture Association of America and the National Association of Theatre Owners now prohibit wearable cameras such as Google Glass. Video provided by Newsy
Powered by NewsLook.com
Spain's New 'Google Tax' Makes News Feeds Pay For Links

Spain's New 'Google Tax' Makes News Feeds Pay For Links

Newsy (Oct. 30, 2014) Spanish lawmakers have passed new IP rules requiring aggregators to pay for linking to news sites, following a broader trend across the E.U. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:

Strange & Offbeat Stories


Space & Time

Matter & Energy

Computers & Math

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins