Featured Research

from universities, journals, and other organizations

New Software Aids Researchers Analyzing Millions Of DNA Sequences

Date:
March 31, 2008
Source:
Boston College
Summary:
As the scope of genome research expands on an almost daily basis, researchers confront increasingly large volumes of data. Now biologists are developing software that enables researchers to analyze millions of DNA sequences faster and with greater accuracy.

It took a global corps of scientists approximately $500 million and 13 years to identify the more than 35,000 genes of the human genome. Five years later, Boston College Biologist Gabor Marth and his research team have developed software that can analyze half a million DNA sequences in 10 minutes.

The Marth laboratory's proprietary PyroBayes software is one of a new breed of computer programs able to accurately process the mountains of genome data flowing from the latest generation of gene decoding machines, which have placed a premium on computational speed and accuracy in data-crunching fields known as bioinformatics and high-throughput biology, said Marth, an associate professor of Biology.

"We're on the edge of a real technological revolution that I think will help us understand the genetic causes of diseases in humans and how genetic materials determine traits in animals," said Marth. "It is going to lead to less expensive technologies that will allow researchers to decode any individual."

PyroBayes will aid researchers involved in the 1,000 Genomes Project, which announced last month a plan to sequence the genomes of 1,000 individuals from around the world. The NIH, which helps direct the project, has awarded Marth more than $1.3 million to develop software over the next four years.

The advances of the Marth lab were revealed in two articles published by the professor and his assistants in the February issue of Nature Methods, the premier journal of scientific research methodology.

In an article co-authored by Marth, post-doctoral researcher Chip Stewart, and graduate students Aaron Quinlan and Mike Strφmberg, the group unveiled the lab's PyroBayes base caller software, which examines data from one of the latest generation of DNA decoding machines -- from Roche / 454 Life Sciences -- faster and with far greater accuracy than other programs for pyrosequencing, a technology that utilizes the detection of pyrophosphate for decoding the sequence of DNA, the carrier of genetic information in living organisms.

A second Nature Methods article, written in collaboration with colleagues from the Washington University School of Medicine, reported that three other computer programs developed by the Marth lab made it possible to quickly and accurately examine the whole genome of a laboratory worm and identify key differences between the sample strain and an earlier strain -- a comparative process known as re-sequencing, now being applied to the genomes of humans and other organisms. This second study used another next-generation DNA sequencing platform, the Illumina/Solexa machine.

Advances are driving re-sequencing costs down, but researchers must still prove the effectiveness of the new technology by working with smaller organisms, which made the worm study critical, Marth said. "This brings us closer to a major milestone in human individual re-sequencing -- the decoding of the genome of human beings in routine fashion," said Marth.

Of the few computer programs available for the new sequencing machines, the software package developed by the Marth lab is the only one capable of working with a variety of decoding machines and offers greater accuracy, allowing researchers to separate true genetic variations from data errors, said Marth. PyroBayes, a Linux-based package, is made available to fellow academic researchers at no cost.

As a member of its analysis group, the Marth lab participates in the data analysis of the 1000 Genomes Project, which was launched last month. The goal of the project is to sequence the genomes of at least 1,000 people from around the world to create the most detailed and medically useful picture to date of human genetic variation.

Ultimately, advances in bioinformatics will help push genetic science forward, shedding new light on human health and disease. Marth sees his lab's role in providing critical tools that help researchers to organize data, interpret them, and visualize genome variations.

"We are excited to develop the software that will help these super-fast, high-throughput sequencing machines to realize their potential to produce invaluable data for research," Marth said.

Journal article can be purchased at Nature Methods: http://www.nature.com/nmeth/journal/v5/n2/full/nmeth.1172.html


Story Source:

The above story is based on materials provided by Boston College. Note: Materials may be edited for content and length.


Cite This Page:

Boston College. "New Software Aids Researchers Analyzing Millions Of DNA Sequences." ScienceDaily. ScienceDaily, 31 March 2008. <www.sciencedaily.com/releases/2008/03/080328070108.htm>.
Boston College. (2008, March 31). New Software Aids Researchers Analyzing Millions Of DNA Sequences. ScienceDaily. Retrieved April 19, 2014 from www.sciencedaily.com/releases/2008/03/080328070108.htm
Boston College. "New Software Aids Researchers Analyzing Millions Of DNA Sequences." ScienceDaily. www.sciencedaily.com/releases/2008/03/080328070108.htm (accessed April 19, 2014).

Share This



More Computers & Math News

Saturday, April 19, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Man Claims He Found Loch Ness Monster With... Apple Maps?

Man Claims He Found Loch Ness Monster With... Apple Maps?

Newsy (Apr. 18, 2014) — Andy Dixon showed the Daily Mail a screenshot of what he believes to be the mythical beast swimming just below the lake's surface. Video provided by Newsy
Powered by NewsLook.com
Facebook Announces Location-Sharing Feature 'Nearby Friends'

Facebook Announces Location-Sharing Feature 'Nearby Friends'

Newsy (Apr. 18, 2014) — Facebook's pending Nearby Friends feature will give users the option to share their nonspecific or specific locations with certain friends. Video provided by Newsy
Powered by NewsLook.com
Michaels Hack Compromises About 3 Million Credit Cards

Michaels Hack Compromises About 3 Million Credit Cards

Newsy (Apr. 18, 2014) — Michaels is now confirming that an eight-month security breach compromised about 3 million customers' credit and debit card data. Video provided by Newsy
Powered by NewsLook.com
Twitter Introduces Facebook-Style App Install Ads

Twitter Introduces Facebook-Style App Install Ads

Newsy (Apr. 17, 2014) — Twitter hopes to make money on app install ads, which has proven to be a successful strategy for Facebook. 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:
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