CUDA-BLASTP is designed to accelerate NCBI BLAST for scanning protein sequence databases by taking advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs. CUDA-BLASTP also has a utility to convert FASTA format database into files readable by CUDA-BLASTP.
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Weiguo Liu, Bertil Schmidt, Wolfgang Müller-Wittig:
“CUDA-BLASTP: accelerating BLASTP on CUDA-enabled graphics hardware“.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011, 8(6): 1678-1684