Algoritmos Paralelos Exatos e Otimizações para Alinhamento de Sequências Biológicas Longas em Plataformas de Alto Desempenho
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Referências
de Figueiredo Jr., M. A. C. (2015). MASA-OpenCL: Comparação Paralela de Sequências Biológicas Longas em GPU. Master’s thesis, Universidade de Brasília, Brasília, Brasil.
de Figueiredo Jr., M. A. C., Sandes, E. F. O., and Melo, A. C. M. A. (2015). Parallel megabase dna sequence comparison with opencl. In 22st International Conference on High Performance Computing, HiPC, pages 436–445.
Durbin, R., Eddy, S., Krogh, A., and Mitchison, G. (2002). Biological sequence analysis. Cambridge University Press.
Gotoh, O. (1982). An improved algorithm for matching biological sequences. Journal of Molecular Biology, 162(3):705–708.
Hirschberg, D. S. (1975). A linear space algorithm for computing maximal common subsequences. Communications of the ACM, 18(6):341–343.
Liu, Y., Schmidt, B., and Maskell, D. (2010). CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized simd abstractions. BMC Research Notes, 3(1):93.
Mount, D. M. (2004). Bioinformatics - sequence and genome analysis (2. ed.). Cold Spring Harbor Laboratory Press.
Myers, E. W. and Miller, W. (1988). Optimal alignments in linear space. Computer applications in the Biosciences, 4(1):11–17.
Needleman, S. B. and Wunsch, C. D. (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology, 48(3):443–453.
Sandes, E. F. O. (2011). Comparação Paralela de Sequ^rncias Biológicas Longas utilizando Unidades de Processamento Gráfico (GPUs). Master’s thesis, Universidade de Brasília, Brasília, Brasil.
Sandes, E. F. O., Boukerche, A., and Melo, A. C. M. A. (2016a). Parallel Exact Pairwise Biological Sequence Comparison: Algorithms, Platforms and Classification. ACM Computing Surveys (accepted).
Sandes, E. F. O. and Melo, A. C. M. A. (2011). Smith-Waterman alignment of huge sequences with GPU in linear space. In IEEE International Parallel Distributed Processing Symposium, pages 1199–1211.
Sandes, E. F. O. and Melo, A. C. M. A. (2013). Retrieving smith-waterman alignments with optimizations for megabase biological sequences using gpu. IEEE Transactions on Parallel and Distributed Systems, 24(5):1009–1021.
Sandes, E. F. O., Miranda, G., , Melo, A. C. M. A., Martorell, X., and Ayguadé, E. (2014a). Fine-grain parallel megabase sequence comparison with multiple heterogeneous GPUs. In Proceedings of the 19th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPoPP ’14, pages 383–384 (short paper).
Sandes, E. F. O., Miranda, G., Martorell, X., Ayguadé, E., Teodoro, G., and Melo, A. C. M. A. (2016b). CUDAlign 4.0: Incremental Speculative Traceback for Exact Chromosome-Wide Alignment in GPU Clusters. IEEE Transactions on Parallel and Distributed Systems, PP(99):1–1.
Sandes, E. F. O., Miranda, G., Martorell, X., Ayguadé, E., Teodoro, G., and Melo, A. C. M. A. (2016c). MASA: a multiplatform architecture for sequence aligners with block pruning. ACM Transactions on Parallel Computing, 2(4):28:1–28:31.
Sandes, E. F. O., Miranda, G., Melo, A. C. M. A., Martorell, X., and Ayguade, E. (2014b). CUDAlign 3.0: Parallel Biological Sequence Comparison in Large GPU Clusters. In IEEE/ACM Symposium on Cluster, Cloud and Grid Computing (CCGrid), pages 160–169.
Sandes, E. F. O., Ralha, C. G., and Melo, A. C. M. A. (2014c). An agent-based solution for dynamic multi-node wavefront balancing in biological sequence comparison. Expert Systems with Applications, 41(10):4929 – 4938.
Sarkar, S., Kulkarni, G., Pande, P., and Kalyanaraman, A. (2010). Network-on-chip hardware accelerators for biological sequence alignment. IEEE Transactions on Computers, 59(1):29–41.
Smith, T. F. and Waterman, M. S. (1981). Identification of common molecular subsequences. Journal of Molecular Biology, 147(1):195–197.
de Figueiredo Jr., M. A. C., Sandes, E. F. O., and Melo, A. C. M. A. (2015). Parallel megabase dna sequence comparison with opencl. In 22st International Conference on High Performance Computing, HiPC, pages 436–445.
Durbin, R., Eddy, S., Krogh, A., and Mitchison, G. (2002). Biological sequence analysis. Cambridge University Press.
Gotoh, O. (1982). An improved algorithm for matching biological sequences. Journal of Molecular Biology, 162(3):705–708.
Hirschberg, D. S. (1975). A linear space algorithm for computing maximal common subsequences. Communications of the ACM, 18(6):341–343.
Liu, Y., Schmidt, B., and Maskell, D. (2010). CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized simd abstractions. BMC Research Notes, 3(1):93.
Mount, D. M. (2004). Bioinformatics - sequence and genome analysis (2. ed.). Cold Spring Harbor Laboratory Press.
Myers, E. W. and Miller, W. (1988). Optimal alignments in linear space. Computer applications in the Biosciences, 4(1):11–17.
Needleman, S. B. and Wunsch, C. D. (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology, 48(3):443–453.
Sandes, E. F. O. (2011). Comparação Paralela de Sequ^rncias Biológicas Longas utilizando Unidades de Processamento Gráfico (GPUs). Master’s thesis, Universidade de Brasília, Brasília, Brasil.
Sandes, E. F. O., Boukerche, A., and Melo, A. C. M. A. (2016a). Parallel Exact Pairwise Biological Sequence Comparison: Algorithms, Platforms and Classification. ACM Computing Surveys (accepted).
Sandes, E. F. O. and Melo, A. C. M. A. (2011). Smith-Waterman alignment of huge sequences with GPU in linear space. In IEEE International Parallel Distributed Processing Symposium, pages 1199–1211.
Sandes, E. F. O. and Melo, A. C. M. A. (2013). Retrieving smith-waterman alignments with optimizations for megabase biological sequences using gpu. IEEE Transactions on Parallel and Distributed Systems, 24(5):1009–1021.
Sandes, E. F. O., Miranda, G., , Melo, A. C. M. A., Martorell, X., and Ayguadé, E. (2014a). Fine-grain parallel megabase sequence comparison with multiple heterogeneous GPUs. In Proceedings of the 19th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPoPP ’14, pages 383–384 (short paper).
Sandes, E. F. O., Miranda, G., Martorell, X., Ayguadé, E., Teodoro, G., and Melo, A. C. M. A. (2016b). CUDAlign 4.0: Incremental Speculative Traceback for Exact Chromosome-Wide Alignment in GPU Clusters. IEEE Transactions on Parallel and Distributed Systems, PP(99):1–1.
Sandes, E. F. O., Miranda, G., Martorell, X., Ayguadé, E., Teodoro, G., and Melo, A. C. M. A. (2016c). MASA: a multiplatform architecture for sequence aligners with block pruning. ACM Transactions on Parallel Computing, 2(4):28:1–28:31.
Sandes, E. F. O., Miranda, G., Melo, A. C. M. A., Martorell, X., and Ayguade, E. (2014b). CUDAlign 3.0: Parallel Biological Sequence Comparison in Large GPU Clusters. In IEEE/ACM Symposium on Cluster, Cloud and Grid Computing (CCGrid), pages 160–169.
Sandes, E. F. O., Ralha, C. G., and Melo, A. C. M. A. (2014c). An agent-based solution for dynamic multi-node wavefront balancing in biological sequence comparison. Expert Systems with Applications, 41(10):4929 – 4938.
Sarkar, S., Kulkarni, G., Pande, P., and Kalyanaraman, A. (2010). Network-on-chip hardware accelerators for biological sequence alignment. IEEE Transactions on Computers, 59(1):29–41.
Smith, T. F. and Waterman, M. S. (1981). Identification of common molecular subsequences. Journal of Molecular Biology, 147(1):195–197.
Publicado
04/07/2016
Como Citar
SANDES, Edans Flávius de Oliveira; DE MELO, Alba Cristina M. A..
Algoritmos Paralelos Exatos e Otimizações para Alinhamento de Sequências Biológicas Longas em Plataformas de Alto Desempenho. In: CONCURSO DE TESES E DISSERTAÇÕES (CTD), 29. , 2016, Porto Alegre.
Anais [...].
Porto Alegre: Sociedade Brasileira de Computação,
2016
.
p. 417-422.
ISSN 2763-8820.
DOI: https://doi.org/10.5753/ctd.2016.9141.
