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CLC bio and SciEngines increase BLAST speed

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Collaboration has begun between CLC bio and SciEngines, a German high-performance computing company, with the aim of completely integrating CLC bio's server- and desktop-based sequence analysis software with SciEngines' FPGA-based Rivyera platform for massively parallel computing. The system will initially feature implementations of nucleotide-nucleotide BLAST (BLASTn), protein-protein BLAST (BLASTp), and Smith-Waterman, with additional algorithms being continuously added.

‘Preliminary BLASTp benchmarks using the tree species Populus trichocarpa, black cottonwood, have demonstrated a 188-times increase in speed using a Rivyera S3-5000 computer with 64 FPGA chips compared to a Xeon E5520 core,’ commented Jost Bissel, chief software architect at SciEngines. ‘The benchmark ran BLASTp to align 920,000 amino acids against a database of one billion amino acids. Similar acceleration has been achieved in early benchmark tests of the BLASTn version, and we expect both BLAST implementations to be accelerated even further before the final release.’

The BLAST software for the Rivyera hardware platform, in which up to 128 FPGAs can be set up in each compute unit, is currently still in development.