Pairwise Sequence Alignment with Gaps with GPU
Department of Computer Science, University of Liverpool, UK
4th International Workshop on Heterogenous and Unconventional Cluster Architectures and Applications (HUCAA), 2015
In this paper we consider the pair-wise sequence alignment problem with gaps, which is motivated by the resequencing problem that requires to assemble short reads sequences into a genome sequence by referring to a reference sequence. The problem has been studied before for single gap and bounded number of gaps. For single gap, there was a GPU-based algorithm proposed. In our work we propose a GPU-based algorithm for the bounded number of gaps case. We implemented the algorithm and compare the performance with the CPU-based algorithm in a multithreadded environment; the results are promising with the GPU version achieving a speedup of 30 times.
October 27, 2015 by hgpu