Pairwise Sequence Alignment with Gaps with GPU

Thomas C. Carroll, Jude-Thaddeus Ojiaku, Prudence W.H. Wong
Department of Computer Science, University of Liverpool, UK
4th International Workshop on Heterogenous and Unconventional Cluster Architectures and Applications (HUCAA), 2015


   title={Pairwise Sequence Alignment with Gaps with GPU},

   author={Carroll, Thomas C and Ojiaku, Jude-Thaddeus and Wong, Prudence WH},



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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.
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