The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.


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.

Download: Google; NVIDIA


  • 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
  • Weiguo Liu, Bertil Schmidt, Yongchao Liu, Wand olfgang Müller-Wittig: "Mapping of the BLASTP algorithm onto GPU clusters". 17th IEEE International Conference on Parallel and Distributed Systems (ICPADS 2011), 2011, 236-243


Our implementation takes advantage of the heterogenous multi-core nature of Cell Broadband Engine (Cell BE) to accelerate the NCBI BLAST for scanning protein sequence databases. Our BLASTP implementation achieves an average speedup of 3.2x compared to the optimized FSA-BLASTP and 3.6x compared to NCBI-BLASTP.


  • A. Wirawan, B. Schmidt, H. Zhang, C.K. Kwoh: "High Performance Protein Sequence Database Scanning on the Cell B.E. Processor". Scientific Programming, 2009, 17(1-2): 97-111