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Table 5 Comparison of two-step procedure with other methodologies

From: A novel approach to identifying regulatory motifs in distantly related genomes

Gene Number of motifs Two-step BS BS Two-step MS MS MAVID TBA
cfos 2 0 0 0 0 0 0
hoxb2 17 8 (+5) 13 2 1 0 0
pax6 6 6 1* 0 0 6 6
scl 5 3 (+1) 1 0 0 0 0
Total 30 17 (+6) 15 2 1 6 6
  1. Number of motifs: the number of motifs reported by Blanchette and Tompa [26] in cfos, Scemama et al. [46] in hoxb2, Kammandel et al. [47] in pax6 and Gƶttgens et al. [48] in scl. Two-step BS: the number of previously described motifs detected by the two-step procedure, combining data reduction and motif detection using BlockSampler. The numbers in parentheses are the number of motifs present in non-significant blocks. BS: the number of previously described motifs detected by BlockSampler in initial full-length datasets. Two-step MS: the number of previously described motifs detected by combining data reduction and motif detection using MotifSampler. MS: the number of previously described motifs detected by MotifSampler in initial full-length datasets. MAVID: the number of previously described motifs detected (correctly aligned) by MAVID. TBA: the number of previously described motifs detected by TBA. *Only part of a motif was detected.