G-PAS 2.0 – Fast GPU vesion of a Pairwise Alignment algorithms

G-PAS 2.0


G-PAS (gpu-pairAlign) implements global and semiglobal Needleman-Wunsch, and Smith-Waterman algorithms with a backtracking procedure which is needed to construct the alignment. Our solution performs the alignment of every given sequence pair, which is a required step e.g. for progressive multiple sequence alignment methods, as well as for DNA recognition at the DNA assembly stage. Tests show that the implementation, with performance up to 6.3 GCUPS on a single GPU for affine gap penalties, is very efficient in comparison to other CPU and GPU-based solutions.


G-PAS Team




  • Linux
  • g++ compiler
  • CUDA 2.0 or higher
  • CUDA-compliant GPU





BMC Bioinformatics. 2011 May 20;12:181.
Protein alignment algorithms with an efficient backtracking routine on multiple GPUs.
Blazewicz J, Frohmberg W, Kierzynka M, Pesch E, Wojciechowski P.

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