Title :
Hardalign: a parallel pairwise alignment hardware application
Author :
Moritz, Guilherme L. ; Lopes, Heitor S. ; Lima, Carlos R Erig
Author_Institution :
Fed. Univ. of Technol., Curitiba
Abstract :
This paper describes the design and implementation of a hardware for parallel pairwise alignment, 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 to evaluate the performance of the system were done for pairs of proteins with up to 2000 amino acids-long. Hardalign was compared with a similar algorithm implemented in software and running in a PC, resulting in a 1:5 speed-up ratio
Keywords :
biomolecular electronics; dynamic programming; field programmable gate arrays; logic design; parallel processing; proteins; reconfigurable architectures; FPGA device; amino acids-long; dynamic programming algorithm; parallel pairwise alignment; pipelined approach; proteins; Amino acids; Bioinformatics; Concurrent computing; Dynamic programming; Field programmable gate arrays; Hardware; Heuristic algorithms; Matrices; Proteins; Sequences;
Conference_Titel :
Field Programmable Technology, 2006. FPT 2006. IEEE International Conference on
Conference_Location :
Bangkok
Print_ISBN :
0-7803-9729-0
Electronic_ISBN :
0-7803-9729-0
DOI :
10.1109/FPT.2006.270350
