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Issue No. 06 - November/December (2011 vol. 8)
ISSN: 1545-5963
pp: 1678-1684
Weiguo Liu , Nanyang Technological University, Singapore
Bertil Schmidt , Nanyang Technological University, Singapore
Wolfgang Müller-Wittig , Nanyang Technological University, Singapore
Scanning protein sequence database is an often repeated task in computational biology and bioinformatics. However, scanning large protein databases, such as GenBank, with popular tools such as BLASTP requires long runtimes on sequential architectures. Due to the continuing rapid growth of sequence databases, there is a high demand to accelerate this task. In this paper, we demonstrate how GPUs, powered by the Compute Unified Device Architecture (CUDA), can be used as an efficient computational platform to accelerate the BLASTP algorithm. In order to exploit the GPU's capabilities for accelerating BLASTP, we have used a compressed deterministic finite state automaton for hit detection as well as a hybrid parallelization scheme. Our implementation achieves speedups up to 10.0 on an NVIDIA GeForce GTX 295 GPU compared to the sequential NCBI BLASTP 2.2.22. CUDA-BLASTP source code which is available at
BLAST, dynamic programming, sequence alignment, graphics hardware, GPGPU, CUDA.

B. Schmidt, W. Müller-Wittig and W. Liu, "CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. , pp. 1678-1684, 2011.
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