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Implementation of a Parallel Algorithm for Protein Pairwise Alignment Using Reconfigurable Computing

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4 Author(s)
Moritz, G.L. ; Bioinformatics Lab. & Electron. Dept., Fed. Univ. of Technol. - Parana, Curitiba ; Jory, C. ; Lopes, H.S. ; Lima, C.R.E.

This paper describes the design and implementation of a parallel pairwise alignment hardware, implemented in a FPGA device. This system is aimed at aligning pairs of proteins, using a dynamic programming algorithm. The alignment is done in parallel thanks to a pipelined approach. All functional blocks are described in detail. Experiments were done to access the performance of the system for up to pairs of 2000-amino acids-long proteins. Hardalign was compared with a similar algorithm implemented in software and running in a PC, resulting in a 1:10 speed-up ratio. Results encourage the continuity of the work, showing that reconfigurable computing can offer interesting solutions for bioinformatics problems

Published in:

Reconfigurable Computing and FPGA's, 2006. ReConFig 2006. IEEE International Conference on

Date of Conference:

Sept. 2006