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Table 1 Running times and sensitivity on simulated sequences containing local alignments of different error rates

From: STELLAR: fast and exact local alignments

error rate 0% 2.5% 5% 7.5% 10%
  time missed time missed time missed time missed time missed
SSEARCH 133:17 h 0.00% 132:55 h 0.00% 133:24 h 0.00% 132:25 h 0.00% 132:52 h 0.00%
STELLAR 2.96 s 0.00% 3.30 s 0.00% 3.61 s 0.00% 3.91 s 0.00% 4.44 s 0.00%
BWT-SW 16.59 s 0.00% 16.63 s 0.00% 16.53 s 0.00% 16.29 s 0.00% 16.24 s 0.00%
BLAST 0.25 s 0.00% 0.26 s 0.16% 0.26 s 5.36% 0.25 s 17.00% 0.24 s 38.80%
BLAST* 0.25 s 0.16% 0.26 s 0.00% 0.28 s 0.04% 0.51 s 0.28% 14.99 s 2.60%
LASTZ 6.49 s 0.00% 6.48 s 0.72% 6.22 s 5.56% 5.86 s 12.68% 5.23 s 24.92%
BLAT 14.30 s 29.36% 11.52 s 29.64% 14.06 s 28.88% 14.71 s 31.44% 14.66 s 34.32%
  1. Sequences have a length of 1 Mb and contain local alignments of lengths between 50 and 200 bp. The simulations were repeated five times, the displayed values are the average of all runs except for SSEARCH which was run only once. Sensitivity is measured by the percentage of missed local alignments (Fig. 8). BWT-SW, BLAST, BLAT, and LASTZ were run with default parameter settings. BLAST* stands for a more sensitive run of BLAST with the word size parameter set to smin, i.e. the minimal length of an ε-core (see text for details).