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Table 3 Speedup for alignment stages of multithreaded muBLASTP over multithreaded NCBI BLAST on Haswell platform (with 24 threads) and Nehalem platform (with 12 threads) with query batches of different query length

From: muBLASTP: database-indexed protein sequence search on multicore CPUs

Query length Haswell platform   Nehalem platform  
  uniprot_sprot env_nr nr uniprot_sprot env_nr nr
  Aver SD Aver SD Aver SD Aver SD Aver SD Aver SD
100 5.7 0.013 2.67 0.013 1.94 0.021 8.2 0.013 4.52 0.017 8.59 0.015
500 3.22 0.012 1.44 0.012 1.39 0.014 2.25 0.018 1.69 0.018 2.69 0.016
1000 2.85 0.016 1.35 0.013 1.20 0.015 1.76 0.018 1.41 0.016 1.72 0.015
Mixed 4.16 0.013 1.41 0.012 1.49 0.012 2.82 0.018 2.34 0.013 4.1 0.015
  1. Aver is the average value of three runs, and SD is the standard deviation of three runs
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