Multiple Sequence Alignment on an FPGA

Authors:
Tim Oliver;Bertil Schmidt;Douglas Maskell;Darran Nathan;Ralf Clemens
Affiliations:
School of Computer Engineering, Nanyang Technological University, Singapore;School of Computer Engineering, Nanyang Technological University, Singapore;School of Computer Engineering, Nanyang Technological University, Singapore;Project Proteus, School of Engineering, Ngee Ann Polytechnic, Singapore;Project Proteus, School of Engineering, Ngee Ann Polytechnic, Singapore
Venue:
ICPADS '05 Proceedings of the 11th International Conference on Parallel and Distributed Systems - Workshops - Volume 02
Year:
2005

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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.