Korilog, an IT specialist that designs solutions facilitating the use of heterogeneous biological information systems, has developed KLAST, a sequence-comparison technology for DNA, RNA and proteins. This technology will underpin new advances in emerging biological fields, be it in relation to the environment, farming, health or biotech.
Korilog, a provider of innovative IT solutions, has launched KLAST, a new high-performance sequence-comparison technology. This technology has stemmed from the company’s collaboration with the GenScale research team at Inria, the government-funded computer-sciences R&D centre based in Rennes, in Britanny (western France). GenScale focuses on the analysis of large-scale genomic data.
KLAST allows specialists to search quickly and accurately for similarities in biological sequences (DNA, RNA and proteins). The technology is specially designed to process the large amounts of data produced by next-generation sequencing.
Patrick Durand, Director at Korilog, explains, “One of the key issues when searching for similarities between sequence databanks is to reduce considerably execution time, while simultaneously maintaining high quality in the resulting data.”
Patrick Durand continues, ”Not only does KLAST meet both of those objectives, but its innovative implementation method takes into account the laboratories’ existing computer infrastructure. Indeed, it reaches accelerations without the need for additional peripherals, as it makes full use of the multicore processors available in standard office computers or in cluster nodes.”
KLASTp performance has achieved acceleration by a factor of 24 as compared to the technology of reference, known as BLASTp. These results were achieved by running both algorithms on the eight cores in an Apple Mac Pro during the comparison of 2,327 proteins from the populus trichocarpa deciduous-tree species.
The experiments were done using the details of 2.9 million proteins held in the database at the National Centre for Biotechnology Information Reference Sequence (NCBI RefSeq). KLAST was proved to be as sensitive and selective as Basic Local Alignment Search Tool (BLAST) and SSEARCH, which is an optimal local-alignment search tool that uses the Smith-Waterman algorithm.
Dominique Lavenier, Genscale Research Team Manager, finds transferring KLAST to a high-tech company such as Korilog is a gratifying and important step for his research team. As Dominique Lavenier explains, “It allows us to contribute directly to new advances in emerging biological fields, ranging from health to farming and the environment. And comments from end-users are highly valuable in maintaining KLAST’s position as a technological leader in intensive sequence comparison.”
In order to supply users with an advanced platform for sequence-similarity research, the KLAST engine is included in Korilog’s ngKLAST graphics software suite and in a plugin for the KNIME data-analysis platform. As a result, users can simultaneously enjoy the KLAST accelerator and the advanced data-analysis functionalities provided by hosting platforms KNIME or ngKLAST.
Through these software solutions, it is therefore possible to operate KLAST either through command lines or through a rich graphic interface, using anything from an individual workstation to a calculation cluster (such as those available at major research facilities).
This new technology can be applied across all aspects of large-scale sequence comparison in a range of sectors, from health, food and bio-defence to the environment and biotechnology.
Korilog is based in north-western France. The company designs innovative IT solutions that closely associate human-computer interfaces, bioinformatics-analysis methods and biological databanks in order to facilitate the use of heterogeneous biological information systems.
For further information about Inria, please go to: http://www.inria.fr/en/centre/rennes
For further information about Korilog, please go to: www.korilog.com
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