An Accelerated Version of NCBI BLAST

NCBI's BLAST application is widely recognized as the most used tool for comparing nucleotide or protein sequences to sequence databases. The Mitrion-C Open Bio Project chose to accelerate this version of BLAST in order to make it possible for the research community to take immediate advantage of faster BLAST searches, while retaining a familiar software environment.

Presently, the project has accelerated the nucleotide search program, BLASTN, and is working on accelerating the protein search program, BLASTP.

How Does it Work?

The Mitrion BLAST application uses the Mitrion Virtual Processor to accelerate the search kernel of the BLASTN algorithm in FPGA hardware. This computationally intense part of the algorithm has been translated into the intrinsically parallel Mitrion-C programming language that is required to program the Mitrion Virtual Processor. The FPGA search kernel is then called from a C host application that runs on a CPU and handles user interaction and data management.
See also the BLAST N Overview section.

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