Featured Research

from universities, journals, and other organizations

Software Tackles Protein Pathways

Date:
September 26, 2003
Source:
Whitehead Institute For Biomedical Research
Summary:
Within 15 seconds, an online software tool contrasts one sequence of DNA with up to 18 million others catalogued in public databases. Now, a software tool developed by Whitehead Institute scientists promises to apply this same computational muscle to the far more intricate world of protein interaction networks, giving researchers a new view of the complexities of cellular life.

CAMBRIDGE, Mass. (Sept. 25, 2003) – When biologists want to compare different sequences of DNA or protein, it's as simple as plugging the information into a browser and pressing enter. Within 15 seconds, an online software tool contrasts one sequence of DNA with up to 18 million others catalogued in public databases. Now, a software tool developed by Whitehead Institute scientists promises to apply this same computational muscle to the far more intricate world of protein interaction networks, giving researchers a new view of the complexities of cellular life.

DNA sequencing technologies allow scientists to easily identify genes and their nucleotide building blocks -- linear strings of information represented by the letters A, C, T and G. The wide accessibility of these technologies has enabled both companies and academic labs to assemble huge libraries of genomic information. Computer engineers, in turn, have helped scientists navigate these oceans of data through tools such as BLAST, the primary software platform that scientists use to compare protein and DNA sequences. However, many researchers believe that the next phase of genomics research will be to map out interaction networks -- the cell's internal wiring system through which genes and proteins communicate.

"The 80s and 90s were about sequences," says Trey Ideker, a former Whitehead Fellow who recently was named an assistant professor of bioengineering at University of California, San Diego. "Now we're starting to see newer types of technologies -- like microarrays -- that allow us to look at how a cell, in its entirety, responds to drugs and other kinds of stimuli. These technologies will revolutionize biology." Already, researchers like Whitehead's Rick Young are beginning to assemble libraries of cellular network pathway maps using microarrays.

"But there's a problem that's not yet addressed," says Whitehead Fellow Brent Stockwell. "What if I've identified a whole protein interaction network in one type of organism and I want to see if a similar network exists in other species?" Until recently, there was no way to do this. It's a need that Stockwell and Ideker hope their new software tool, called PathBLAST, will meet.

At the core of PathBLAST is a program that can represent these interaction networks mathematically. The program is based on algorithms that scientists use to represent chemical structures. "An interaction network, in its form, is essentially like a chemical structure," says Stockwell, "and fortunately there are already a great set of tools for representing chemical structures." Developed by Brian Kelley, a software engineer in Stockwell's lab, this algorithm translates all the information from an entire interaction network into a linear code. Using an interface developed by Whitehead's Biocomputing group, PathBLAST can rapidly compare interaction networks from different organisms.

In research published this week in the online edition of the Proceedings of the National Academy of Sciences, Ideker and Stockwell took the entire genomes from the yeast S. cerevisiae and the bacterium H. pylori and compared the interaction networks in both organisms. The software crunched the numbers and displayed the results in seconds. The turnaround time was impressive considering the scope of the effort: the bacterium contained 1,465 interactions among 732 proteins: the yeast contained 14,489 interactions among 4,688 proteins.

The study revealed that one pathway critical in catalyzing DNA replication and another one instrumental in protein degradation were conserved in both organisms as a single network. "What was surprising was that there was one network, not two," Ideker says. "So now the question is, 'What's the attraction between these two complexes?'"

At the moment, there's no clear answer. But as labs continue to do these types of experiments, there eventually could be a huge payoff in comparing such things as viral networks to human networks, possibly allowing drug companies to develop products that target cellular pathways unique to viruses.

As for other applications, it's still too early to tell, Ideker says. "It's like asking in 1985, 'What's the impact of gene sequencing going to be?' We're trying to get the basic mechanisms in place to eventually do these kinds of comparisons."

To access PathBLAST, visit http://www.pathblast.org.


Story Source:

The above story is based on materials provided by Whitehead Institute For Biomedical Research. Note: Materials may be edited for content and length.


Cite This Page:

Whitehead Institute For Biomedical Research. "Software Tackles Protein Pathways." ScienceDaily. ScienceDaily, 26 September 2003. <www.sciencedaily.com/releases/2003/09/030926065217.htm>.
Whitehead Institute For Biomedical Research. (2003, September 26). Software Tackles Protein Pathways. ScienceDaily. Retrieved July 23, 2014 from www.sciencedaily.com/releases/2003/09/030926065217.htm
Whitehead Institute For Biomedical Research. "Software Tackles Protein Pathways." ScienceDaily. www.sciencedaily.com/releases/2003/09/030926065217.htm (accessed July 23, 2014).

Share This




More Matter & Energy News

Wednesday, July 23, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Government Approves East Coast Oil Exploration

Government Approves East Coast Oil Exploration

AP (July 18, 2014) The Obama administration approved the use of sonic cannons to discover deposits under the ocean floor by shooting sound waves 100 times louder than a jet engine through waters shared by endangered whales and turtles. (July 18) Video provided by AP
Powered by NewsLook.com
Sunken German U-Boat Clearly Visible For First Time

Sunken German U-Boat Clearly Visible For First Time

Newsy (July 18, 2014) The wreckage of the German submarine U-166 has become clearly visible for the first time since it was discovered in 2001. Video provided by Newsy
Powered by NewsLook.com
Obama: U.S. Must Have "smartest Airports, Best Power Grid"

Obama: U.S. Must Have "smartest Airports, Best Power Grid"

Reuters - US Online Video (July 17, 2014) President Barak Obama stopped by at a lunch counter in Delaware before making remarks about boosting the nation's infrastructure. Mana Rabiee reports. Video provided by Reuters
Powered by NewsLook.com
Crude Oil Prices Bounce Back After Falling Below $100 a Barrel

Crude Oil Prices Bounce Back After Falling Below $100 a Barrel

TheStreet (July 16, 2014) Oil Futures are bouncing back after tumbling below $100 a barrel for the first time since May yesterday. Jeff Grossman is the president of BRG Brokerage and trades at the NYMEX. Grossman tells TheStreet the Middle East is always a concern for oil traders. Oil prices were pushed down in recent weeks on Libya increasing its production. Supply disruptions in Iraq fading also contributed to prices falling. News from China's economic front showing a growth for the second quarter also calmed fears on its slowdown. Jeff Grossman talks to TheStreet's Susannah Lee on this and more on the Energy Department's Energy Information Administration (EIA) report. Video provided by TheStreet
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:
from the past week

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