Genomic sequences processed in minutes

A new computational tool developed at the US Department of Energy’s Pacific Northwest National Laboratory is speeding up understanding of complex genomic sequences.

ScalaBLAST is a “sequence alignment tool” that can divide the work of analysing biological data into manageable fragments so large data sets can run on many processors simultaneously. The technology means large-scale problems, such as the analysis of an organism, can be solved in minutes, rather than weeks.

In the world of high-end computing, researchers assemble systems composed of many processors but without special modifications, software doesn’t run any faster on it than it would on a personal computer. In order to get answers to complicated biological questions more quickly, PNNL researchers “parallelised” the software using Global Arrays, a powerful programming toolkit, by creating algorithms to distribute the work.

PNNL researchers say ScalaBLAST may be used to process complex genomic sequences, work that is essential to understanding the building blocks of the genome, or rather, how they work and fit together. Genomes represent an organism’s entire DNA, including its genes. When the gene’s sequences are analysed they can provide clues to diseases and possible treatments.

Using ScalaBLAST, researchers can manage the large influx of data resulting from new questions that arise during human genome research. Prior to this new tool, it took researchers 10 days to analyse one organism. Now, researchers can analyse 13 organisms within nine hours.

“Access to and understanding the pieces of genome sequences will allow researchers to understand the body’s cellular machinery and discover clues to some types of cancer. And it will help in developing drugs or detection methods to be used for particular diseases,” said T.P. Straatsma, a PNNL senior research scientist.

“It’s fair to say that, in the realm of human health and disease, if you can solve a problem in one area, you can often solve it in others – that’s the nature of human biology,” Straatsma added.