Pairwise Sequence Alignment with Gaps with GPU

In this paper we consider the pair-wise sequence alignment problem with gaps, which is motivated by the re-sequencing 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.