Navigation Links
New approach to 'spell checking' gene sequences
Date:5/21/2012

A PhD student from CSIRO and the University of Queensland has found a better way to 'spell check' gene sequences.

The student, Lauren Bragg, has contributed to the May issue of the prestigious journal Nature Methods highlighting her new approach and its software implementation called Acacia.

Acacia analyses the output of next-generation gene sequencing instruments which read the four-letter alphabet of As, Cs, Ts and Gs the 'bases' that code for DNA and spell out the genes of different living organisms. Acacia specifically applies to important parts of microbe genes called amplicons.

Just as a computer spell checker finds typing errors in words, so Acacia finds errors in the DNA code of amplicon sequences produced during gene sequencing.

Acacia shows clear improvements over the two error-correction tools currently used by biologists for amplicon sequences and it's easier for biologists to use.

Ms Bragg's development of Acacia is part of the field of bioinformatics, a blend of computer science, statistics and biology. Despite her surname, however, she is modest about her achievements.

"It's exciting to be published in a journal like Nature Methods but I get more satisfaction from hearing how my software is helping biologists fix sequencing errors." she said.

Machine errors in the long lengths of A, C, G and T code can cause biologists to misinterpret which genes are there, or which microbial species might exist in a environmental samples from, say, a waste water treatment plant or from the ocean or even our guts.

Acacia works by using the statistical theory of likelihoods to analyse the code for DNA bases which may have been mistakenly added or deleted common errors in gene sequencing.

"The Nature article is our way of telling the international biology community that there's a new software tool they can use for error-correcting that's pretty easy to use, quick and reliable".

"That way, they won't think they've discovered a new microbe species when they haven't or overlooked one they should have found", she said.

The method, or algorithm, that Acacia uses took 18 months for Ms Bragg to fully develop and test.


'/>"/>
Contact: Carrie Bengston
Carrie.Bengston@csiro.au
61-293-253-224
CSIRO Australia
Source:Eurekalert

Related biology news :

1. Scripps Florida scientist awarded $1.5 million to design therapeutics with new RNA approach
2. Manatee hearing good enough to sense approaching motorboats
3. Approach to diabetes self-management too narrow, study suggests
4. UofL research holds promise of therapeutic approach for gum disease
5. A project to research biological and chemical aspects of microalgae to fuel approach
6. Stanford scientists develop gene therapy approach to grow blood vessels in ischemic limbs
7. Wild west approach to claiming the oceans genetic resources must end: UBC media release
8. Using online patient communities and new trial approaches to optimize clinical research
9. Gut microbe networks differ from norm in obese people, systems biology approach reveals
10. A new way of approaching the early detection of Alzheimers disease
11. Industry, regulators should take system safety approach to offshore drilling in aftermath of Deepwater Horizon accident, says new report
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:11/14/2016)... Nov. 14, 2016  xG Technology, Inc. ("xG" or ... critical wireless communications for use in challenging operating environments, ... 30, 2016. Management will hold a conference call to ... p.m. Eastern Time (details below). Key Recent ... $16 million binding agreement to acquire Vislink Communication Systems. ...
(Date:6/22/2016)... On Monday, the Department of Homeland Security (DHS) issued ... the Biometric Exit Program. The Request for Information (RFI), ... that CBP intends to add biometrics to confirm when ... , in order to deter visa overstays, to ... Logo - http://photos.prnewswire.com/prnh/20160622/382209LOGO ...
(Date:6/9/2016)... control systems is proud to announce the introduction of fingerprint attendance control software, allowing ... are actually signing in, and to even control the opening of doors. ... ... ... Photo - http://photos.prnewswire.com/prnh/20160609/377487 ...
Breaking Biology News(10 mins):
(Date:11/30/2016)... ... November 30, 2016 , ... BEI Kimco, ... Actuator with a flexure design that ensures high alignment accuracy by preventing unwanted ... is ideally suited where extreme precision is required, such as in medical equipment, ...
(Date:11/30/2016)... Nov. 30, 2016 Biotest Pharmaceuticals Corporation (BPC), ... to announce the addition of its newest plasma collection ... Nebraska . The 15,200 square foot state-of-the-art facility ... 2016 and brings the total number of BPC,s plasma ... Carlisle , BPC,s Chief Executive Officer said "We are ...
(Date:11/30/2016)... and BEIJING , Nov. ... leading commercial provider of genomic services and solutions with ... today that it has completed a USD $75 Million ... Bank Co., Ltd.,s CMB International Capital Management ( ... Investment Management Co., Ltd. ("SDIC Innovation") and Shanghai Sigma ...
(Date:11/30/2016)... ... ... SSCI, the established leader in small-molecule cocrystal technology and development, will again ... pharmaceutical cocrystals as drug substance . The Lunch and Learn will take ... the successful November 15th event that took place in Burlingame, CA. Eyal H. Barash, ...
Breaking Biology Technology: