G-PAS 2.0-an improved version of protein alignment tool with an efficient backtracking routine on multiple GPUs

Bulletin of the Polish Academy of Sciences: Technical Sciences

Volumn 60, Issue 3, 2012, Pages 491-494

  Frohmberg, W ^a   Kierzynka, M ^a,c   Blazewicz, J ^a,b   Wojciechowski, P ^a  

^a POZNAN UNIVERSITY OF TECHNOLOGY   (Poland)

^b INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

^c POZNAN SUPERCOMPUTING AND NETWORKING CENTER   (Poland)

Author keywords

Alignment with backtracking procedure; GPU computing; Pairwise alignment

Indexed keywords

COMPUTATIONAL ARCHITECTURE; GPU COMPUTING; GPU-BASED; GRAPHICS PROCESSING UNIT; HIGH-THROUGHPUT; MULTIPLE GPUS; PAIRWISE ALIGNMENT; PROTEIN ALIGNMENT;

COMPUTER GRAPHICS; TOOLS;

PROGRAM PROCESSORS;

EID: 84882350295     PISSN: 02397528     EISSN: None     Source Type: Journal    
DOI: 10.2478/v10175-012-0062-1     Document Type: Article

References (28)

1. M. Ciznicki, M. Kierzynka, K. Kurowski, B. Ludwiczak, K. Napierala, and J. Palczynski, "Efficient isosurface extraction using marching tetrahedra and histogram pyramids on multiple GPUs", Lecture Notes in Computer Science 7204, 343-352 (2012
2. M. Blazewicz, S.R. Brandt, M. Kierzynka, K. Kurowski, B. Ludwiczak, J. Tao, and J. Weglarz, "CaKernel - a parallel application programming framework for heterogenous computing architectures", Scientific Programming 19 (4), 185-197 (2011
3. W. Jendernalik, J. Jakusz, G. Blakiewicz, R. Piotrowski, and S. Szczepanski, "CMOS realisation of analogue processor for early vision processing", Bull. Pol. Ac.: Tech. 59 (2), 141-147 (2011
4. L. Ligowski and W. Rudnicki, "An efficient implementation of Smith Waterman algorithm on GPU using CUDA, for massively parallel scanning of sequence databases", IPDPS doi:10.1109/IPDPS.2009.5160931 (2009
5. Y. Liu, D.L. Maskell and B. Schmidt, "CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDAenabled GPUs based on SIMT and virtualized SIMD abstractions", BMC Research Notes 3, 93 (2010
6. S.A. Manavski and G. Valle, "CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment", BMC Bioinformatics 9 (2), S10 (2008
7. L. Ligowski, W.R. Rudnicki, Y. Liu, and B. Schmidt, "Accurate scanning of sequence databases with the Smith-Waterman algorithm", GPU Computing Gems, Emerald Edition 1, 155-157 (2011
8. J. Blazewicz, W. Frohmberg, M. Kierzynka, and P. Wojciechowski, "G-MSA - A GPU-based, fast and accurate algorithm for multiple sequence alignment", J. Parallel and Distributed Computing, doi:10.1016/j.jpdc.2012. 04.004 (2012
9. K. Kwarciak and P. Formanowicz, "A greedy algorithm for the DNA sequencing by hybridization with positive and negative errors and information about repetitions" Bull. Pol. Ac.: Tech. 59 (1), 111-115 (2011
10. J. Blazewicz, P. Formanowicz, F. Guinand, M. Kasprzak, "A heuristic managing errors for DNA sequencing", Bioinformatics 18, 652-660 (2002
11. J. Blazewicz, W. Frohmberg, M. Kierzynka, E. Pesch, and P. Wojciechowski, "Protein alignment algorithms with an efficient backtracking routine on multiple GPUs", BMC Bioinformatics 12, 181 (2011
12. S.B. Needleman and C.D.Wunsch, "A general method applicable to the search for similarities in the amino acid sequence of two proteins", J. Mol. Biol. 48 (3), 443-53 (1970
13. T.F. Smith and M.S. Waterman, "Identification of Common Molecular Subsequences", J. Molecular Biology 147, 195-97 (1981
14. O. Gotoh, "An improved algorithm for matching biological sequences", J. Molecular Biology 162, 705-708 (1981
15. K.-M. Chao, W. R. Pearson, and W. Miller, "Aligning two sequences within a specified diagonal band", Comput. Appl. Biosci. 8 (5), 481-487 (1992
16. M. Gribskov, A.D. McLachlan, and D. Eisenberg, "Profile analysis: detection of distantly related proteins", PNAS 84, 4355-4358 (1987
17. M. Gribskov, R. Luthy, and D. Eisenberg, "Profile analysis", Methods in Enzymology 183, 146-159 (1990
18. M.S. Waterman, "Sequence alignments in the neighborhood of the optimum with general application to dynamic programming", PNAS 80, 3123-3124 (1983
19. M.S. Waterman and T.H. Byers, "A dynamic programming algorithm to find all solutions in a neighborhood of the optimum", Math. Biosci. 77, 179-188 (1985
20. D. Naor and D. Burtlag, "On suboptimal alignment of biological sequences", Proc. 4th Annual Symposium on Combinatorial Pattern Matching 1, 179-196 (1993
21. M. Zuker, "Suboptimal sequence alignment in molecular biology, alignment with error analysis", J. Mol. Biol. 221, 403-420 (1991
22. M. Vingron and P. Argos, "Determination of reliable regions in protein sequence alignments", Protein Engin. 7, 565-569 (1990
23. A.J. Viterbi, "Error bounds for convolutional codes and an asymptotically optimal decoding algorithm", IEEE Trans. Inf. Theory IT-13, 260-269 (1967
24. D. Zhang, "An implementation of Viterbi algorithm on GPU", First Int. Conf. on Information Science and Engineering 1, CD-ROM (2009
25. Z. Du, Z. Yin and D.A. Bader, "A tile-based parallel Viterbi algorithm for biological sequence alignment on GPU with CUDA", Ninth IEEE Int. Workshop on High Performance Computational Biology Atlanta, GA 1, CD-ROM (2010
26. E.W. Myers and W. Miller, "Optimal alignments in linear space", Comput. Appl. Biosci. 4 (1), 11-17 (1988
27. R.L. Graham, "Bounds on multiprocessing timing anomalies", SIAM J. Appl. Math. 17 (2), 416-429 (1969
28. J. Blazewicz, K. Ecker, E. Pesch, G. Schmidt, and J. Weglarz, Handbook on Scheduling: From Theory to Applications, Springer, Berlin, 2007.