Implementation of Smith-Waterman algorithm in OpenCL for GPUs

Proceedings of the 9th Int. Workshop on Parallel and Distributed Methods in Verification, PDMC 2010 - Joint with the 2nd Int. Workshop on High Performance Computational Systems Biology, HiBi 2010

Volumn , Issue , 2010, Pages 48-56

  Razmyslovich, Dzmitry ^a   Marcus, Guillermo ^a   Gipp, Markus ^a   Zapatka, Marc ^b   Szillus, Andreas ^b  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

Bioinformatics; CUDA; GPU; OpenCL; Smith Waterman

Indexed keywords

CANCER RESEARCH; CUDA; GPU; OPENCL; QUERY SEQUENCE; SEQUENCE ALIGNMENTS; SEQUENCE LENGTHS; SMITH-WATERMAN; SMITH-WATERMAN ALGORITHM; TARGET APPLICATION;

ALGORITHMS; BIOINFORMATICS; COMPUTATIONAL COMPLEXITY; PROGRAM PROCESSORS;

DISTRIBUTED COMPUTER SYSTEMS;

EID: 79951802332     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/PDMC-HiBi.2010.16     Document Type: Conference Paper

References (16)

1. K. Robison, "Application of second-generation sequencing to cancer genomics." Briefings in bioinformatics, pp. bbq013+, April 2010. [Online]. Available: http://dx.doi.org/10.1093/bib/bbq013
2. M. R. Stratton, P. J. Campbell, and P. A. Futreal, "The cancer genome," Nature, vol. 458, no. 7239, pp. 719-724, April 2009. [Online]. Available: http://dx.doi.org/10.1038/nature07943
3. "International network of cancer genome projects," Nature, vol. 464, no. 7291, pp. 993-998, April 2010. [Online]. Available: http://dx.doi.org/10.1038/nature08987
4. H. Li and N. Homer, "A survey of sequence alignment algorithms for next-generation sequencing," Brief Bioinform, pp. bbq015+, May 2010. [Online]. Available: http://dx.doi.org/10.1093/bib/bbq015
5. C. Ling, K. Benkrid, and T. Hamada, "A parameterisable and scalable smith-waterman algorithm implementation on cuda-compatible gpus," Application Specific Processors, 2009. SASP '09. IEEE 7th Symposium on, pp. 94-100, jul. 2009.
6. Y. Liu, B. Schmidt, and D. L. Maskell, "Cudasw++2.0: enhanced smith-waterman protein database search on cuda-enabled gpus based on simt and virtualized simd abstractions." BMC Res Notes, vol. 3, p. 93, 2010. [Online]. Available: http://www.biomedsearch.com/nih/CUDASW20-enhanced-Smith- Waterman-protein/20370891.html
7. M. Farrar, "Striped smith-waterman speeds database searches six times over other simd implementations," Bioinformatics, vol. 23, no. 2, pp. 156-161, 2007.
8. S. Manavski and G. Valle, "Cuda compatible gpu cards as efficient hardware accelerators for smith-waterman sequence alignment," BMC Bioinformatics, vol. 9, no. Suppl 2, p. S10, 2008. [Online]. Available: http://www.biomedcentral.com/1471-2105/9/S2/S10
9. T. F. Smith and M. S. Waterman, "Identification of common molecular subsequences," Journal of Molecular Biology, vol. 147, pp. 195-197, 1981.
10. S. Henikoff and J. G. Henikoff, "Amino acid substitution matrices from protein blocks." Proceedings of the National Academy of Sciences of the United States of America, vol. 89, no. 22, pp. 10 915-10 919, November 1992. [Online]. Available: http://dx.doi.org/10.1073/pnas.89.22.10915
11. M. O. Dayhoff and R. M. Schwartz, "Chapter 22: A model of evolutionary change in proteins," in in Atlas of Protein Sequence and Structure, 1978.
12. "Khronos Group," 2008. [Online]. Available: http://www.khronos.org
13. NVIDIA, NVIDIA OpenCL Programming Guide for the CUDA Architecture, Version 2.3, 2010.
14. -, NVIDIA OpenCL Best Practices Guide, Version 2.3, 2009.
15. "National Center for Biotechnology Information (NCBI)." [Online]. Available: http://www.ncbi.nlm.nih.gov
16. "DAAD - German Academic Exchange Service." [Online]. Available: http://www.daad.de