Design and implementation of a highly parameterised FPGA-based skeleton for pairwise biological sequence alignment

Proceedings 2007 IEEE Symposium on Field-Programme Custom Computing Machines, FCCM 2007

Volumn , Issue , 2007, Pages 275-277

  Benkrid, Khaled ^a   Liu, Ying ^a   Benkrid, Abdsamad ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

C (PROGRAMMING LANGUAGE); COMPUTERS; DNA SEQUENCES; FIELD PROGRAMMABLE GATE ARRAYS (FPGA); INTEGRATED CIRCUIT DESIGN; MUSCULOSKELETAL SYSTEM; PARAMETERIZATION; PROTEINS;

BIOLOGICAL SEQUENCE ALIGNMENT; DESIGN AND IMPLEMENTATIONS; HARDWARE IMPLEMENTATIONS; NEEDLEMAN-WUNSCH ALGORITHM; PROCESSING ELEMENTS; PROTEIN SEQUENCE ALIGNMENTS; SEQUENCE ALIGNMENTS; SMITH-WATERMAN ALGORITHM;

BIOINFORMATICS;

EID: 47349107082     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/FCCM.2007.6     Document Type: Conference Paper

References (8)

1. Durbin, R., Eddy, S., Krogh, A., and Mitchison, G., 'Biological Sequence Analysis: Probabilistic Models for Proteins and Nucleic Acids', Cambridge University Press, Cambridge UK, 1998
2. Smith, T.F. and Waterman, M.S. Identification of common molecular subsequences. J. Mol. Biol., 147, pp.195-197, 1981
3. Altschul, S. F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. 'Basic Local Alignment Search Tool', Journal of Molecular Biology, 215, pp. 403-410, 1990.
4. Borah, M., Bajwa, R.S., Hannenhalli, S., and Irwin, M.J. 'A SIMD solution to the sequence comparison problem on the MGAP', ASAP'94 Proceedings, IEEE Computer Science, pp. 144-160, 1994
5. Guerdoux-Jamet, P., Lavenier, D. 'SAMBA: hardware accelerator for biological sequence comparison', Computer Applications in Biosciences, CABIOS, 12 (6), pp. 609-615, 1997.
6. Yamaguchi, Y., Maruyama, T., and Konagaya, A. 'High Speed Homology Search with FPGAs', Proceedings of the Pacific Symposium on Biocomputing, pp.271-282, 2002.
7. VanCourt, T. and Herbordt, M. C. 'Families of FPGA-Based Algorithms for Approximate String Matching', Proceedings of Application-Specific Systems, Architectures, and Processors, ASAP'04, pp. 354-364, 2004
8. Oliver, T., Schmidt, B. and Maskell, D. 'Hyper customized processors for bio-sequence database scanning on FPGAs', Proceedings of the 2005 ACM/SIGDA 13th international symposium on Field-programmable gate arrays