Now showing items 1-6 of 6

    • CUDAlign 3.0: Parallel biological sequence comparison in large GPU clusters 

      De Sandes, Edans; Miranda Álamo, Guillermo; De Melo, Alba Cristina Magalhaes Alves; Martorell Bofill, Xavier; Ayguadé Parra, Eduard (Institute of Electrical and Electronics Engineers (IEEE), 2014)
      Conference report
      Restricted access - publisher's policy
      This paper proposes and evaluates a parallel strategy to execute the e+ xact Smith-Waterman (SW) biological sequence comparison algorithm for huge DNA sequences in multi-GPU platforms. In our strategy, the computation of ...
    • CUDAlign 4.0: incremental speculative traceback for exact chromosome-wide alignment in GPU clusters 

      De Sandes, Edans; Miranda, Guillermo; Martorell Bofill, Xavier; Ayguadé Parra, Eduard; Teodoro, George; de Melo, Alba (2016-10-01)
      Article
      Open Access
      This paper proposes and evaluates CUDAlign 4.0, a parallel strategy to obtain the optimal alignment of huge DNA sequences in multi-GPU platforms, using the exact Smith-Waterman (SW) algorithm. In the first phase of CUDAlign ...
    • Fine-grain parallel megabase sequence comparison with multiple heterogeneous GPUs 

      De Sandes, Edans; Miranda Álamo, Guillermo; Melo, Alba; Martorell Bofill, Xavier; Ayguadé Parra, Eduard (Association for Computing Machinery (ACM), 2014)
      Conference report
      Restricted access - publisher's policy
      This paper proposes and evaluates a parallel strategy to execute the exact Smith-Waterman (SW) algorithm for megabase DNA sequences in heterogeneous multi-GPU platforms. In our strategy, the computation of a single huge ...
    • Fine-grain parallel megabase sequence comparison with multiple heterogeneous GPUs 

      De Sandes, Edans; Miranda Álamo, Guillermo; De Melo, Alba Cristina Magalhaes Alves; Martorell Bofill, Xavier; Ayguadé Parra, Eduard (2014-08-01)
      Article
      Restricted access - publisher's policy
      This paper proposes and evaluates a parallel strategy to execute the exact Smith-Waterman (SW) algorithm for megabase DNA sequences in heterogeneous multi-GPU platforms. In our strategy, the computation of a single huge ...
    • Formalization of block pruning: reducing the number of cells computed in exact biological sequence comparison algorithms 

      De Sandes, Edans; Teodoro, George; Walter, Maria Emilia; Martorell Bofill, Xavier; Ayguadé Parra, Eduard; Melo, Alba (Wiley Heyden, 2018-05-01)
      Article
      Open Access
      Biological sequence comparison algorithms that compute the optimal local and global alignments calculate a dynamic programming (DP) matrix with quadratic time complexity. The DP matrix H is calculated with a recurrence ...
    • MASA: a multi-platform architecture for sequence aligners with block pruning 

      De Sandes, Edans; Miranda, Guillermo; Martorell, Xavier; Ayguadé Parra, Eduard; Teodoro, George; de Melo, Alba (2016-03-01)
      Article
      Open Access
      Biological sequence alignment is a very popular application in Bioinformatics used routinely worldwide. Many implementations of biological sequence alignment algorithms have been proposed for multicores, GPUs, FPGAs and ...