Skip to main content

Table 2 Summary of CUDAlign versions

From: DNA sequences alignment in multi-GPUs: acceleration and energy payoff

Version Major contributions Ref.
1.0 Uses SW with affine gap (Gotoh) to compare long sequences on GPUs. It ouputs the optimal score and the end coordinates of the optimal alignment. [50]
2.0 Includes an adapted version of Myers-Miller to retrieve the optimal alignment in linear space. [51]
2.1 Block pruning optimization. [29]
3.0 Multi-GPU version for SW phase 1 (distributes the matrix, overlaps computations with communications). [49]
4.0 Multi-GPU version for SW phases 1 and 2, including Incremental Speculative Traceback (IST) to accelerate the multi-GPU retrieval of the optimal alignment. [30]
MASA Multi-platform architecture for sequence aligner, enabling versions to run on (1) multicore CPU using OpenMP, (2) multicore CPU using OmpsSs, (3) manycore GPU using CUDA, and (4) Xeon Phi using OpenMP. [52]