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Table 6 Assessment of RefSelect on large data sets

From: RefSelect: a reference sequence selection algorithm for planted (l, d) motif search

t k DNA Sequences Protein Sequences
time time a N original /N improved time time a N original /N improved
50 3 0.5 s 0.4 s 2.37 0.4 s 0.4 s 15.79
100 5 2.0 s 1.9 s 2.56 1.8 s 1.7 s 15.41
200 10 8.2 s 8.0 s 1.85 7.3 s 7.1 s 14.20
300 15 18.6 s 18.1 s 2.43 16.2 s 15.9 s 18.31
400 20 33.5 s 32.5 s 2.52 28.7 s 27.9 s 18.42
500 25 52.4 s 50.6 s 2.78 44.9 s 43.5 s 16.64
600 30 75.8 s 73.5 s 2.56 66.8 s 64.8 s 15.98
  1. s: seconds; time and time a: the running time of RefSelect and that of the first step of RefSelect; N original and N improved : the number of candidate motifs generated from the first k original input sequences and that for the k reference sequences selected by RefSelect.