Researchers have developed a new
bioinformatics tool to ‘spell check’ gene sequences and help biologists better
understand the natural world.
Researchers
from CSIRO and the University of Queensland have developed a new bioinformatics
tool called Acacia to ‘spell check’ gene sequences for their accuracy.
In the
May issue of the journal Nature Methods, the paper’s lead author,
Ms. Lauren Bragg, a Ph.D. student at CSIRO and the University of Queensland,
highlights her new approach and its software implementation.
Acacia
analyzes 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. The software
specifically applies to important parts of microbe genes called amplicons.
The
method, or algorithm, that Acacia uses took 18 months for Ms. Bragg to fully
develop and test.
Just as
a computer spell checker finds typing errors in words, Acacia finds errors in
the DNA code of amplicon sequences produced during gene sequencing. According
to the authors, Acacia shows clear improvements over the two error-correction
tools currently used by biologists for amplicon sequences and is easier to use.
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
an environmental sample. Acacia works by using the statistical theory of
likelihoods to analyze common errors in sequencing, such as DNA bases which may
have been mistakenly added or deleted.
“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
article can be found at: Bragg L et al. (2012) Fast,
accurate error-correction of amplicon pyrosequences using Acacia.
Source: CSIRO.
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