NDLI: A Reconfigurable Accelerator for Parallel Longest Common Protein Subsequence Algorithm

Content Provider	IEEE Xplore Digital Library
Author	Sahoo, B. Padhy, S.
Copyright Year	2009
Description	Author affiliation: Department of CSE & IT, KIIT University, Bhubaneswar - 751024, India (Sahoo, B.) \|\| Department of Mathematics, Utkal University, Bhubaneswar - 751004, India (Padhy, S.)
Abstract	The problem of longest common subsequence is defined as finding the longest subsequence common to two input sequences. It can be employed in many fields such as speech and signal processing, data compression, syntactic pattern recognition, string processing (bioinformatics), and genetic engineering. This paper describes the design of a parallel longest common protein subsequence hardware, implemented in a FPGA device, using a dynamic programming (DP) algorithm. Such algorithms have computational complexity proportional to the length product of both involved sequences. Usually, lengths of both input sequences are very long, resulting in long processing time. The data dependency in DP imposes a serious constraint on the algorithm, not allowing its direct parallelization. To alleviate this serious problem, a reconfigurable accelerator for DP algorithm is presented. The main features include: a multistage PE (processing element) design with even stage delay which significantly reduces the FPGA resource usage and hence allows more parallelism to be exploited; and a pipelined control mechanism. Basing on these two techniques, the proposed accelerator can reach at 82-MHz frequency in an Altera EP1S30 device. This accelerator provides more than 660 speedup as compared to a standard desktop platform with a 2.8-GHz Xeon processor and 4-GB memory. Results show that reconfigurable computing can offer interesting solutions for bioinformatics problems.
Starting Page	260
Ending Page	265
File Size	4224464
Page Count	6
File Format	PDF
ISBN	9781424429271
DOI	10.1109/IADCC.2009.4809018
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2009-03-06
Publisher Place	India
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Algorithm design and analysis Protein engineering Signal processing algorithms Data compression Genetic engineering Pattern recognition Bioinformatics Speech processing Field programmable gate arrays Biomedical signal processing
Content Type	Text
Resource Type	Article

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