Navigation Links
Software developed by Boston College lab delivers speed and accuracy to genome research
Date:3/27/2008

CHESTNUT HILL, MA 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 laboratorys 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.

Were 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 Strmberg, the group unveiled the labs 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 labs 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.


'/>"/>

Contact: Ed Hayward
ed.hayward@bc.edu
617-552-4826
Boston College
Source:Eurekalert

Related biology news :

1. Futronic Announces Microsoft Vista and Windows 2008 Server Support for Its Fingerprint Logon Software
2. M2SYS Introduces Revolutionary Biometric Artificial Intelligence Technology to Significantly Reduce Fingerprint Software False Reject Rates
3. LOGICARE Selects M2SYS Biometric Fingerprint Software to Ensure Patient Privacy and Protect Confidential Information
4. Software Techniques Inc. Selects M2SYS Fingerprint Software to Meet Continuous Growth and Demand for Desktop Biometric Time & Attendance Solutions
5. Titanium Group Signs Letter of Intent to Acquire Multimilion Dollar Medical Software Company and Its Existing Sales Network
6. Titanium Group Signs Letter of Intent to Acquire Multimilion Dollar Medical Software Company and Its Existing Sales Network
7. CIC Again Named to Software Magazines Annual Prestigious Software 500 List
8. Aware, Inc. Introduces Biometrics Software for Tenprint Autocapture
9. Radiant Systems Selects BIO-key(R) Biometric Software for POS Solution
10. IdentiPHI Re Launches SAFmodule Software to Secure Novell(R) Networks
11. IdentiPHI Re Launches SAFmodule Software to Secure Novell(R) Networks
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:11/29/2016)... Nearly one billion matches per second with DERMALOG,s high-speed AFIS    ... ... DERMALOG is Germany's largest Multi-Biometric supplier: The company's Fingerprint ... ... Multi-Biometric supplier: The company's Fingerprint Identification System is part of an efficient ...
(Date:11/21/2016)... VILNIUS, Lithuania , Nov. 21, 2016 /PRNewswire/ ... identification and object recognition technologies, today announced that ... for smart cards was submitted for the ... and successfully passed all the mandatory steps of ... III evaluation is a continuing test of fingerprint ...
(Date:11/15/2016)... , Nov. 15, 2016  Synthetic Biologics, Inc. ... therapeutics focused on the gut microbiome, today announced ... 25,000,000 shares of its common stock and warrants ... at a price to the public of $1.00 ... Synthetic Biologics from the offering, excluding the proceeds, ...
Breaking Biology News(10 mins):
(Date:12/8/2016)... , ... December 08, 2016 , ... ... FrontPanel SDK that provide essential device-to-computer interconnect using USB or PCI Express, announced ... FrontPanel support. The FOMD-ACV-A4 is a small, thin, SODIMM-style module that fits a ...
(Date:12/8/2016)... , ... December 08, 2016 ... ... the commercial launch of flexible packaging for their exceptionally efficient human mesenchymal ... system extends RoosterBio’s portfolio of bioprocess media products engineered to radically streamline ...
(Date:12/8/2016)... Fla. , Dec. 8, 2016  HedgePath ... company that discovers, develops and plans to commercialize ... its shares of common stock were approved for ... will begin trading on the OTCQX, effective today, ... qualify for the OTCQX market, companies must meet ...
(Date:12/7/2016)... , ... December 07, 2016 , ... ... its phase I/II dose escalation and expansion clinical trial for its lead drug ... Austria. The purpose of the trial was to determine the safety, antitumor activity, ...
Breaking Biology Technology: