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BLAST N Overview
BLAST P Overview
SGI RASC Implementation
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.
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