New approach to 'spell checking' gene sequences

May 10, 2012

(Phys.org) -- A PhD student from CSIRO and the University of Queensland has found a better way to 'spell check' gene sequences and help biologists better understand the natural world.

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 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 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 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 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 .

"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.

Now it's nose to the grindstone to get the thesis done.

Explore further: New insights into how different tissues establish their biological and functional identities

add to favorites email to friend print save as pdf

Related Stories

Adapting crops and 'natives' to a changing climate

Jul 26, 2011

(PhysOrg.com) -- CSIRO scientists are investigating the potentially damaging effects climate change will have on Australia’s agricultural crops and native plants as carbon dioxide concentrations, temperatures ...

Preventing dangerous nonsense in human gene expression

Oct 13, 2011

Human genes are preferentially encoded by codons that are less likely to be mistranscribed (or "misread") into a STOP codon. This finding by Brian Cusack and colleagues from the Max Planck Institute for Molecular Genetics ...

Recommended for you

Deadly human pathogen Cryptococcus fully sequenced

22 hours ago

Within each strand of DNA lies the blueprint for building an organism, along with the keys to its evolution and survival. These genetic instructions can give valuable insight into why pathogens like Cryptococcus ne ...

User comments : 0

More news stories

Researchers successfully clone adult human stem cells

(Phys.org) —An international team of researchers, led by Robert Lanza, of Advanced Cell Technology, has announced that they have performed the first successful cloning of adult human skin cells into stem ...

Plants with dormant seeds give rise to more species

Seeds that sprout as soon as they're planted may be good news for a garden. But wild plants need to be more careful. In the wild, a plant whose seeds sprouted at the first warm spell or rainy day would risk disaster. More ...

Researchers develop new model of cellular movement

(Phys.org) —Cell movement plays an important role in a host of biological functions from embryonic development to repairing wounded tissue. It also enables cancer cells to break free from their sites of ...

Male monkey filmed caring for dying mate (w/ Video)

(Phys.org) —The incident was captured by Dr Bruna Bezerra and colleagues in the Atlantic Forest in the Northeast of Brazil.  Dr Bezerra is a Research Associate at the University of Bristol and a Professor ...