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Table 1 Motif discovery example.

From: Discovering multiple realistic TFBS motifs based on a generalized model

Sequences S

SIM A

TFBSs R

PFM Θ (4 × w(= 7))

S1: acgtCGATTGCctaag

0000100000000000

CGATTGC

 

S2: taTGATCGAtgacgca

0010000000000000

TGATCGA

A: 0.0 0.2 0.6 0.1 0.1 0.0 0.7

S3: cgaCAATTGAgcttac

0001000000000000

CAATTGA

C: 0.8 0.0 0.2 0.3 0.3 0.2 0.3

S4: gCGCTCGAcaagctgt

0100000000000000

CGCTCGA

G: 0.0 0.8 0.0 0.0 0.0 0.8 0.0

S5: cgttTGTCACAgtcta

0000100000000000

TGTCACA

T: 0.2 0.0 0.2 0.6 0.6 0.0 0.0

S6: tcagcCACACCCagct

0000010000000000

CACACCC

 

S7: ccagagCGTCTGAttg

0000001000000000

CGTCTGA

Background: Θ0:

S8: gacttcaCGACTGAgc

0000000100000000

CGACTGA

θ0A= 0.24 θ0C= 0.29

S9: gctgcccatCGATTGA

0000000001000000

CGATTGA

θ0G= 0.24 θ0T= 0.23

S10: ccaggtacCGATTGCa

0000000010000000

CGATTGC

 
  1. An artificial example of motif discovery. It shows the sequences S, the SIM A, the motif instances R, the PFM Θ and the background frequencies Θ0. In sequences S, the nucleotides from the background are shown in lower case, while the nucleotides from the motif instances in upper case.