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2008

Accelerating String Set Matching in FPGA Hardware for Bioinformatics Research

9 years 7 months ago
Accelerating String Set Matching in FPGA Hardware for Bioinformatics Research
Background: This paper describes techniques for accelerating the performance of the string set matching problem with particular emphasis on applications in computational proteomics. The process of matching peptide sequences against a genome translated in six reading frames is part of a proteogenomic mapping pipeline that is used as a case-study. The Aho-Corasick algorithm is adapted for execution in field programmable gate array (FPGA) devices in a manner that optimizes space and performance. In this approach, the traditional Aho-Corasick finite state machine (FSM) is split into smaller FSMs, operating in parallel, each of which matches up to 20 peptides in the input translated genome. Each of the smaller FSMs is further divided into five simpler FSMs such that each simple FSM operates on a single bit position in the input (five bits are sufficient for representing all amino acids and special symbols in protein sequences). Results: This bit-split organization of the Aho-Corasick imple...
Yoginder S. Dandass, Shane C. Burgess, Mark Lawren
Added 08 Dec 2010
Updated 08 Dec 2010
Type Journal
Year 2008
Where BMCBI
Authors Yoginder S. Dandass, Shane C. Burgess, Mark Lawrence, Susan M. Bridges
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