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

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4 Author(s)
Guilherme L. Moritz ; Bioinformatics Laboratory (CPGEI) & Electronics Department, Federal University of Technology ¿ Paraná, Av. 7 de setembro, 3165 80230-901 Curitiba (PR) ¿ Brazil ; Cristiano Jory ; Heitor S. Lopes ; Carlos R. Erig Lima

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:

2006 IEEE International Conference on Reconfigurable Computing and FPGA's (ReConFig 2006)

Date of Conference:

20-22 Sept. 2006