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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 Göttgens 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.