NDLI: Multiple Sequence Alignment on an FPGA

Content Provider	IEEE Xplore Digital Library
Author	Oliver, T. Schmidt, B. Nathan, D. Clemens, R. Maskell, D.
Copyright Year	2005
Description	Author affiliation: Sch. of Comput. Eng., Nanyang Technol. Univ. (Oliver, T.; Schmidt, B.)
Abstract	Molecular biologists frequently compute multiple sequence alignments (MSAs) to identify similar regions in protein families. Progressive alignment is a widely used approach to compute MSAs. However, aligning a few hundred sequences by popular progressive alignment tools requires several hours on sequential computers. Due to the rapid growth of biological sequence databases biologists have to compute MSAs in a far shorter time. In this paper we present a new approach to MSA on reconfigurable hardware platforms to gain high performance at low cost. To derive an efficient mapping onto this type of architecture, fine-grained parallel processing elements (PEs) have been designed. Using this PE design as a building block we have constructed a linear systolic array to perform a pairwise sequence distance computation using dynamic programming. This results in an implementation with significant runtime savings on a standard off-the-shelf FPGA
Sponsorship	IEEE Comput. Soc. TCDP and TCPP Fukuoka Inst. of Technol. (FIT)
Starting Page	326
Ending Page	330
File Size	190037
Page Count	5
File Format	PDF
ISBN	0769522815
ISSN	15219097
DOI	10.1109/ICPADS.2005.202
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2005-07-20
Publisher Place	Japan
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Field programmable gate arrays Biology computing Proteins Databases Hardware Performance gain Costs Computer architecture Parallel processing Systolic arrays
Content Type	Text
Resource Type	Article
Subject	Hardware and Architecture

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