Algoritmos Paralelos Exatos e Otimizações para Alinhamento de Sequências Biológicas Longas em Plataformas de Alto Desempenho

  • Edans Flávius de Oliveira Sandes UnB
  • Alba Cristina M. A. de Melo UnB

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Referências

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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.

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04/07/2016
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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. 67-72. ISSN 2763-8820. DOI: https://doi.org/10.5753/ctd.2016.9141.