Desktop hardware-acceleration
Version 1.06 - Released December 17
Through innovative use of FPGA technology we have created a Cube which runs Smith Waterman up to 125 times faster than a 3 GHz desktop computer, and acceptably close to the speed of BLAST. Smith Waterman searches taking 14 hours on the desktop are thus reduced to around 7 minutes on the Cube.
This is a breakthrough for desktop-based bioinformatics, as it gives researchers the possibility of running BLAST-like searches of a significantly higher quality than before.
Improve quality as well
Our comparison between BLAST and Smith Waterman shows that running BLASTp with the default expectation value of 10 often results in only half as many hits as running a Smith Waterman search on the Cube. So by using the Cube instead of BLAST, you'll improve the quality of the data you're working with!
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