New genome assembly tool brings complex DNA research to the desktop

June 28, 2011

Genome assembly, the construction of DNA sequences from sample sequences, has received a boost with the release of Gossamer, a tool which allows researchers to assemble DNA fragments using cheap commodity computers rather than supercomputers.

New DNA are revolutionising biology. These technologies can read billions of short fragments of DNA in a matter of days, producing DNA sequence information in unprecedented volumes and at ever increasing rates. These fragments of DNA come from cells of different types and conditions and can be analyzed to help answer important biological questions. For example, to gain a detailed understanding of many aspects of cancer, it is important to determine how the DNA of the has been rearranged.

To answer such questions it is often necessary to piece together the billions of fragments to reconstruct the underlying DNA sequence – a process called genome assembly. Existing programs for assembling such DNA fragments tend to require very large amounts of computer memory, necessitating large and expensive computing infrastructure. The NICTA Computational Genomics team has developed a prototype assembler called Gossamer that demonstrates how a human genome can be assembled on cheap commodity computers. The Gossamer prototype assembler was demonstrated today at Bio 2011 in Washington, the world’s largest biotechnology event. The tool is now available to be trialled for non-commercial use.

Professor Terry Caelli, Director of NICTA’s Health Business Area, described Gossamer as a wonderful example of how computer science can play a fundamental role in progressing life sciences research. “Gossamer is a breakthrough for the genome research community that helps overcome the significant infrastructure requirements the average laboratory is unable to access,” he said. “We are making a prototype version of the tool available to the research community to assist them in progressing their important genome research.”

Explore further: Blending bacterial genomes for megacloning

Related Stories

Researchers Discover New Way to Store Information Via DNA

February 20, 2008

Researchers at UC Riverside have found a way to get into your body and your bloodstream. No, they’re not spiritual gurus or B-movie mad scientists. Nathaniel G. Portney, Yonghui Wu, Stefano Lonardi, and Mihri Ozkan from ...

New cheaper method for mapping disease genes

May 27, 2008

Scientists at the Swedish medical university Karolinska Institutet have developed a new DNA-sequencing method that is much cheaper than those currently in use in laboratories. They hope that this new method will make it possible ...

Researchers develop 'hi-def' copy number variation decoder

November 1, 2010

University of Toronto researchers have developed a new "high definition" computer program to analyze human DNA and more accurately detect genetic variants that affect individual traits like disease susceptibility and varying ...

Recommended for you

Plastic in 99 percent of seabirds by 2050

August 31, 2015

Researchers from CSIRO and Imperial College London have assessed how widespread the threat of plastic is for the world's seabirds, including albatrosses, shearwaters and penguins, and found the majority of seabird species ...

Researchers unveil DNA-guided 3-D printing of human tissue

August 31, 2015

A UCSF-led team has developed a technique to build tiny models of human tissues, called organoids, more precisely than ever before using a process that turns human cells into a biological equivalent of LEGO bricks. These ...

Study shows female frogs susceptible to 'decoy effect'

August 28, 2015

(Phys.org)—A pair of researchers has found that female túngaras, frogs that live in parts of Mexico and Central and South America, appear to be susceptible to the "decoy effect." In their paper published in the journal ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.