Implementation of a parallel algorithm for protein pairwise alignment using reconfigurable computing

Proceedings of the 2006 IEEE International Conference on Reconfigurable Computing and FPGA's, ReConFig 2006

Volumn , Issue , 2006, Pages 99-105

  Moritz, Guilherme L ^a   Jory, Cristiano ^a   Lopes, Heitor S ^a   Lima, Carlos R Erig ^a  

^a UNIVERSIDADE TECNOLÓGICA FEDERAL DO PARANÁ   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

ALIGNMENT; AMINES; AMINO ACIDS; BIOINFORMATICS; BIOMOLECULES; BOOLEAN FUNCTIONS; DYNAMIC PROGRAMMING; FIELD PROGRAMMABLE GATE ARRAYS (FPGA); MATHEMATICAL PROGRAMMING; ORGANIC ACIDS; PROTEINS; SYSTEMS ENGINEERING;

DYNAMIC PROGRAMMING (DP) ALGORITHMS; FPGA DEVICES; FUNCTIONAL BLOCKS; INTERNATIONAL CONFERENCES; PAIRWISE ALIGNMENT; RE CONFIGURABLE COMPUTING (RCC); RUNNING IN; SPEED UPS;

PARALLEL ALGORITHMS;

EID: 34548089761     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/RECONF.2006.307759     Document Type: Conference Paper

References (11)

1. Altera Corporation, NIOS II Processor Reference Handbook, 2005.
2. M. Canella, F. Miglioli, A. Bogliolo, E. Petraglio and E. Sanchez, "Performing DNA comparison on a bio-inspired tissue of FPGAs," in Proc. of IEEE International Parallel and Distributed Processing Symposium, pp. 193-199, 2003.
3. K. Compton, "Reconfigurable computing: a survey of systems and software," A CM Computing Surveys, vol. 34, no. 2, pp. 171-210, 2002.
4. S. Henikoff and J.G. Henikoff, "Amino acid substitution matrices from protein blocks," PNAS, vol. 89, pp. 10915-10919, 1992.
5. nd ed., Prentice-Hall, Dorset, 2001.
6. H.S. Lopes and G.L. Moritz, "A distributed approach for a multiple sequence alignment algorithm using parallel virtual machine," In: Proceedings of 27th Int. Conf. of IEEE EMBS, Shanghai, China, pp. 2843-2846, 2005.
7. A. Marongiu, P. Palazzari, V. Rosato, V., "Designing hardware for protein sequence analysis, Bioinformatics, vol. 19, pp. 1739-1740, 2003.
8. S.B. Needleman and CD. Wunsch, "A general method applicable to the search for similarities in the amino acid sequence of two proteins," Journal of Molecular Biology, vol. 48, pp. 433-443, 1970.
9. T. Oliver, B. Schmidt, D. Nathan, R. Clemens, and D. Maskell, "Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW," Bioinformatics, vol. 21, pp. 3431-3432, 2005.
10. M.S. Waterman, T.F. Smith, and W.A. Beyer, "Some biological sequence metrics," Advances in Mathematics, vol. 20, pp. 367-387, 1976.
11. Y. Yamaguchi, T. Maruyama and A. Konagaya, "High speed homology search with FPGAs," In: Proc. Pacific Symposium on Biocomputing, pp. 271-282, 2002.