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Convey turns volume up to 11 on Smith-Waterman algorithm

That’s a Spinal Tap reference, for you young readers out there (catch up on the cultural reference here).

Convey Computer announced this week that they’ve completed an implementation of the Smith-Waterman algorithm, an important algorithm in bioinformatics, and that it’s fast

Convey Computer logoConvey Computer Corporation announced today that its implementation of the Smith-Waterman algorithm, widely used in life sciences applications for aligning DNA and protein sequences, is 172x faster than conventional methods and represents the fastest Smith-Waterman implementation to date.

The footnote on “the fastest Smith-Waterman implementation to date” is that Convey compared its algorithms to SSEARCH in FASTA in internal benchmarking on an Intel Nehalem core using the SIMD SSE2 instruction set.

In case your memory isn’t fresh on Convey’s approach, they are one of the few companies making a major push in HPC to bring FPGAs into the mainstream of high end computing with a hybrid hardware/software approach

Convey’s revolutionary hybrid-core computing architecture tightly integrates advanced computer architecture and compiler technology with commercial, off-the-shelf hardware – namely an Intel Xeon processor and Xilinx Field Programmable Gate Arrays (FPGAs). The systems help customers reduce energy costs associated with high-performance computing, while dramatically increasing performance over industry standard servers. Additionally, Convey systems are easy for programmers to use because they provide full support of an ANSI standard C, C++ and FORTRAN development environment.

More on the algorithm, and on its use at the University of South Carolina with the Department of Computer Science and Engineering, in the article linked above.

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