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:1/21/2016)... India , January 21, 2016 ... According to a new market research report "Emotion Detection ... and Others), Software Tools (Facial Expression, Voice Recognition ... Regions - Global forecast to 2020", published by ... is expected to reach USD 22.65 Billion by ...
(Date:1/18/2016)... , Jan. 18, 2016  Extenua Inc., a ... simplifies the use and access of ubiquitous on-premise ... partnership with American Cyber.  ... experience leading transformational C4ISR and Cyber initiatives in ... the latest proven technology solutions," said Steve ...
(Date:1/11/2016)... Jan. 11, 2016 Synaptics Incorporated (NASDAQ: ... today announced that its ClearPad ® TouchView ™ ... won two separate categories in the 8 th ... Best Technology Breakthrough. The Synaptics ® TDDI solution ... supply chain, thinner devices, brighter displays and borderless designs. ...
Breaking Biology News(10 mins):
(Date:2/4/2016)... Columbia and MENLO PARK, Calif. ... (OTCQX: DMPI) ("DelMar" and the "Company"), a biopharmaceutical company focused ... announced that it will present at the 18 th ... February 8, 2016 at 10:00 a.m. EST in ... , DelMar,s president and CEO, will provide an update on ...
(Date:2/4/2016)... ... 2016 , ... Franz Inc. , an early innovator ... been recognized As “ Best in Semantic Web Technology - USA & Leader ... it’s our priority to showcase prominent professionals who are excelling in their industry ...
(Date:2/3/2016)... 3, 2016  With the growing need for ... is underway, therapies such as monoclonal antibodies, recombinant ... host of indications are in high demand. Conventionally ... development and production of these therapeutics. However, due ... high costs, novel approaches and novel expression systems ...
(Date:2/3/2016)... ... February 03, 2016 , ... ProMIS Neurosciences is currently in ... to misfolded, propagating strains of Amyloid beta involved in Alzheimer’s disease. The Company ... , Following on from the first misfolded Amyloid beta target announced on Nov. ...
Breaking Biology Technology: