A major bugaboo in the genomics field is that errors often exist in draft sequences after DNA molecules are decoded and assembled. Researchers in Singapore say their algorithm can nip this problem in the bud, saving scientists from chasing dead ends in error-laden sequences and streamlining how genomes are pieced together after sequencing.
The Genome Institute of Singapore said its computational tool, called Opera, has an unmatched guarantee that the software can reconstruct sequences of genomes reliably, and the algorithm is capable of performing well when tackling large datasets, InSciences reports. Niranjan Nagarajan, assistant director of computational and mathematical biology at the institute, led the project, which was detailed in the November issue of the Journal of Computational Biology.
Opera is being made freely available as the number of genomes that are sequenced is growing rapidly, with technologies making it relatively fast and cheap to sequence DNA. Bracing themselves for the data tsunami resulting from this trend, researchers are looking for ways to inject automation and systematic tools into the work that is done after DNA is sequenced.
"Opera is an important advance in genome assembly algorithms--currently it is the best stand-alone genome scaffolder available in the community," said Mihai Pop, an associate professor in the department of computer science at the University of Maryland, as quoted by InSciences. "In Opera, Dr. Nagarajan's team has introduced a rigorous theoretical framework for genome scaffolding as well as a practical implementation that achieves remarkable performance."