Accelerating string set matching in FPGA hardware for bioinformatics research.

BMC Bioinformatics
Yoginder S DandassSusan M Bridges

Abstract

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). This bit-split organization of the Aho-Corasick implementation enables efficient utilization of the limited random access memory (RAM) resources available in typical FPGAs. The use of on-chip RAM as opposed to FPGA logic resources for FSM implementation also enables rapid reconfiguration of the FPGA without the place and...Continue Reading

References

May 23, 2002·Bioinformatics·Adalberto T CasteloGuang R Gao
Jan 20, 2004·Proteomics·Jacob D JaffeGeorge M Church
Jun 25, 2004·Nucleic Acids Research·Michael BrudnoBurkhard Morgenstern
Aug 4, 2004·Genome Research·Jacob D JaffeGeorge M Church
Nov 30, 2004·Computers in Biology and Medicine·Heikki HyyröMauno Vihinen
Feb 22, 2005·Rapid Communications in Mass Spectrometry : RCM·Anish T AlexChristopher W V Hogue
Sep 21, 2005·BMC Genomics·Dário E KalumeAkhilesh Pandey
Apr 6, 2006·Proteomics·Fiona M McCarthyShane C Burgess
Feb 6, 2007·Bioinformatics·Istvan BogdanRobert J Beynon

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Citations

Jul 22, 2011·Journal of Bioinformatics and Computational Biology·Marc Thuillard, Vincent Moulton
Apr 26, 2011·BMC Bioinformatics·William S SandersShane C Burgess
Dec 31, 2009·PLoS Computational Biology·Joel T Dudley, Atul J Butte
Sep 29, 2009·Protein Engineering, Design & Selection : PEDS·Xiao-Bo WangNai-Yang Deng
May 26, 2010·Rapid Communications in Mass Spectrometry : RCM·Leheng WangSi-Min He
Oct 10, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Edward B FernandezWalid A Najjar

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Software Mentioned

PROMO
Windows XP
SITEBLAST
ACA
Snort
Xilinx
AhoPro
XST
CLUSTALW

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