Figure S3: All results for artificial data set (position distribution = gauss; given length = true). For each data set, we show the nucleotide precison recal curve, the ...
Figure S3: All results for artificial data set (position distribution = gauss; given length = true). For each data set, we show the nucleotide precison recal curve, the sequence logo obtained from each of the tools, and the position distribution learned by Dispom. Finally, we show a simplified overview of these results.
1
2
3
4
5
6
7
8
9
2 1.5 1 0.5 0 1
2
3
4
Position
5
6
7
8
9
0.0
0.2
1.0
1
2
3
4
Position
5
6
7
8
0.0
0.2
0.4 0.6 0.8 Nucleotide Recall
1.0
9
1
2
3
4
5
Position
6
7
8
9
0.2
0.4 0.6 0.8 Nucleotide Recall
1.0
2 1.5 1 0.5 0
10
1
2
3
4
Position
5
6
7
8
9
0.2
0.4 0.6 0.8 Nucleotide Recall
1.0
2 1.5 1 0.5 0 1
2
3
4
5
Position
6
7
8
9
Nucleotide Precision 0.2 0.4 0.6 0.8
Nucleotide Precision 0.2 0.4 0.6 0.8
DME MEME Dispom
0.0
0.2
0.4 0.6 0.8 Nucleotide Recall
1.0
2 1.5 1 0.5 0
10
1
2
3
4
Position
5
6
7
8
9
0.0
0.2
0.4 0.6 0.8 Nucleotide Recall
1.0
2 1.5 1 0.5 0
10
DME Dispom
IMPROBIZER DEME A−GLAM
0.0
DEME
0.0
WEEDER
1.0
1.0
1.0 0.0
10
Dispom MEME GIBBS SAMPLER DEME IMPROBIZER
0.0
DEME
0.0 0.0
2 1.5 1 0.5 0
Nucleotide Precision 0.2 0.4 0.6 0.8
Nucleotide Precision 0.2 0.4 0.6 0.8
Nucleotide Precision 0.2 0.4 0.6 0.8 0.0
Nucleotide Precision 0.2 0.4 0.6 0.8
0.4 0.6 0.8 Nucleotide Recall
2 1.5 1 0.5 0
10
WEEDER
DME
MA0077
0.0
Information content
1.0
IMPROBIZER
DEME
Dispom
MA0054
Information content
0.4 0.6 0.8 Nucleotide Recall
Dispom
Information content
0.2
A−GLAM MEME DEME
MA0052
DME
Information content
0.0
10
DEME
Dispom
Information content
2 1.5 1 0.5 0
IMPROBIZER
Information content
1.0
Information content
PR-curve
0.4 0.6 0.8 Nucleotide Recall
Information content
0.2
A−GLAM
0.0
DEME
DME
DME
0.0
WEEDER
DME
0.0
Information content
Dispom
0.0
WEEDER
Dispom
Nucleotide Precision 0.2 0.4 0.6 0.8
Nucleotide Precision 0.2 0.4 0.6 0.8
Dispom
0.0
Nucleotide Precision 0.2 0.4 0.6 0.8
DME DME
MA0048-ma52unif 1.0
MA0048-ma52gauss 1.0
MA0048 1.0
MA0015 1.0
MA0005-1 1.0
1.0
MA0001-1
1
2
3
4
Position
5
6
7
8
0.2
0.4 0.6 0.8 Nucleotide Recall
1.0
2 1.5 1 0.5 0
9
1
2
3
Position
4
5
6
7
8
6
7
8
6
7
8
6
7
8
6
7
8
6
7
8
6
7
8
6
7
8
6
7
8
Position
2
3
4
5
6
7
8
9
10
1
2
3
4
5
6
7
6
7
8
1
2
3
4
5
8
9
10
1
2
3
4
5
7
8
9
10
1
no prediction
Position
2 1.5 1 0.5 0
Position
6
6
7
8
2 1.5 1 0.5 0
9
1
2
3
4
5
Position
6
7
8
9
Information content
Information content
9
Information content
2 1.5 1 0.5 0
Position
5
2 1.5 1 0.5 0
no prediction
2 1.5 1 0.5 0
10
1
2
3
4
Position
5
6
7
8
9
2 1.5 1 0.5 0
10
1
2
3
4
5
Position
6
7
2
3
4
no prediction
8
9
2 1.5 1 0.5 0
10
1
2
3
4
Position
5
6
7
5
6
7
8
2 1.5 1 0.5 0
9
1
2
3
Position
8
9
2 1.5 1 0.5 0
10
1
2
3
4
Position
5
4
5
Position
Information content
4
Information content
2 1.5 1 0.5 0 1
3
Position
Information content
Information content
Information content
A-GLAM
2
no prediction
Information content
1
no prediction
2 1.5 1 0.5 0
Information content
2 1.5 1 0.5 0
Information content
Information content
Information content
true PWM
6
7
8
2 1.5 1 0.5 0
9
1
2
3
Position
4
5
Position
1
2
3
4
5
6
7
8
9
10
1
2
3
4
Position
5
6
7
8
9
10
1
2
3
4
Position
5
6
7
8
9
1
2
3
4
5
Position
6
7
8
9
10
1
2
3
4
Position
5
6
7
8
9
10
1
2
3
4
5
Position
6
7
8
9
2 1.5 1 0.5 0
10
1
2
3
4
Position
5
6
7
8
9
Information content
2 1.5 1 0.5 0
Information content
2 1.5 1 0.5 0
Information content
2 1.5 1 0.5 0
Information content
2 1.5 1 0.5 0
Information content
2 1.5 1 0.5 0
Information content
2 1.5 1 0.5 0
Information content
Information content
Information content
DEME 2 1.5 1 0.5 0
10
1
2
3
4
Position
5
6
7
8
2 1.5 1 0.5 0
9
1
2
3
Position
4
5
Position
3
4
2
3
4
5
6
7
8
9
10
1
3
4
5
6
9
10
1
2
3
4
2
3
4
5
6
7
8
9
7
8
9
10
1
2
3
4
5
6
6
7
8
1
2
3
4
5
1
2
3
4
5
7
8
9
6
7
8
1
2
3
4
5
8
9
10
1
2
3
4
1
2
3
4
5
6
6
7
8
7
8
9
10
1
1
2
3
4
5
6
7
8
9
10
2
3
4
5
2
3
4
5
6
7
8
9
10
1
2
3
4
5
6
7
8
9
10
1
2
3
4
Position
7
8
9
1
2
3
4
5
6
7
8
9
7
8
9
10
1
1
2
3
4
5
6
7
8
9
10
Information content 1
2
3
4
5
2
3
4
5
6
7
8
9
7
8
9
10
1
2
3
4
5
6
7
8
9
10
1
2
3
1
2
3
4
5
7
8
9
6
7
8
9
1
2
3
1
2
3
4
5
4
5
Position
2 1.5 1 0.5 0
10
5
2 1.5 1 0.5 0
Position
Position
4
Position
2 1.5 1 0.5 0
10
2 1.5 1 0.5 0
Position
6
2 1.5 1 0.5 0
Position
Position
2 1.5 1 0.5 0
10
6
2 1.5 1 0.5 0
Position
Position
5
Position
2 1.5 1 0.5 0
10
2 1.5 1 0.5 0
Position
6
Information content
Information content 1
Position
2 1.5 1 0.5 0
9
6
2 1.5 1 0.5 0
Position
Position
5
Position
2 1.5 1 0.5 0
9
2 1.5 1 0.5 0
10
7
Position
Position
Position
6
Information content
Information content
9
2 1.5 1 0.5 0
10
2 1.5 1 0.5 0
Position
5 Position
Information content
Information content
Information content 2
8
Position
2 1.5 1 0.5 0 1
7
2 1.5 1 0.5 0
Position
Improbizer
6
Information content
Information content
Information content
2 1.5 1 0.5 0 1
5
Position
Information content
2
2 1.5 1 0.5 0
Information content
1
Information content
10
2 1.5 1 0.5 0
Information content
9
Information content
8
Information content
7
2 1.5 1 0.5 0
Information content
6
2 1.5 1 0.5 0
Information content
5
Position
Information content
4
2 1.5 1 0.5 0
Information content
3
Information content
2
Gibbs Sampler
2 1.5 1 0.5 0
Information content
1
2 1.5 1 0.5 0
Information content
2 1.5 1 0.5 0
Information content
Information content
Information content
DME
6
7
8
2 1.5 1 0.5 0
9
1
2
3
Position
4
5
Position
1
2
3
4
5
6
7
8
9
10
1
2
3
4
5
6
7
8
9
10
2
3
0.000 −101
−1
4
5
6
7
8
−501
−401
5
−301 −201 Position
−101
−1
6
7
8
9
1
−401
2
3
4
1
2
3
4
5
6
−101
−1
7
8
9
10
−501
−401
7
8
●
9
10
−101
●
●
2
3
4
5
1
2
3
4
5
6
−1
7
8
9
−501
−401
7
8
9
1
●
c(0, 1) ●
DEME c(0, 1) ●
●
DME c(0, 1) ●
●
GIBBS SAMPLER c(0, 1) ●
●
IMPROBIZER c(0, 1) ●
●
MEME c(0, 1) ●
●
WEEDER c(0, 1) ●
●
Dispom c(0, 1) ●
c(0, 1)
c(0, 1)
2 1.5 1 0.5 0
10
1
−101
−1
●
●
c(0, 1)
3
4
2
3
4
5
6
c(0, 1)
−501
−401
7
7
8
9
8
9
1
1
2
3
4
5
6
−301 −201 Position
−101
−1
●
●
●
●
c(0, 1)
c(0, 1)
c(0, 1)
−401
3
7
8
9
2 1.5 1 0.5 0
10
1
2
3
4
5
6
−301 −201 Position
−1
5
7
8
2 1.5 1 0.5 0
9
1
2
Position
−101
4
Position
3
4
5
Position
0.006 0.005 0.004 0.003 0.002 0.001 0.000
0.008 0.006 0.004 0.002 0.000 −501
2
no prediction
2 1.5 1 0.5 0
10
2 1.5 1 0.5 0
10
Position
●
●
c(0, 1)
6
0.008 0.006 0.004 0.002 0.000
●
●
5
Position
●
A−GLAM c(0, 1)
2
Position
−301 −201 Position
●
●
Information content
10
0.020 0.015 0.010 0.005 0.000
●
●
6
Position
Position
−301 −201 Position
●
Information content 1
0.020 0.015 0.010 0.005 0.000
●
●
6
2 1.5 1 0.5 0
Position
−301 −201 Position
5
Position
0.020 0.015 0.010 0.005 0.000 −501
Information content
10
2 1.5 1 0.5 0
9
0.012 0.010 0.008 0.006 0.004 0.002 0.000
0.002 −301 −201 Position
4
Position
0.004
−401
Information content 1
0.006
−501
3
Position
2 1.5 1 0.5 0
Position
0.012 0.010 0.008 0.006 0.004 0.002 0.000
Position
2 1.5 1 0.5 0
Position
Dispom
2
Information content
1
no prediction Information content
Information content
Information content
2 1.5 1 0.5 0
Information content
10
2 1.5 1 0.5 0
Information content
9
Information content
8
MA0077
7
c(0, 1)
6
MA0054
5
Position
MA0052
4
c(0, 1)
3
Information content
2
2 1.5 1 0.5 0
c(0, 1) MA0048+MA0052(unif)
1
c(0, 1) MA0048+MA0052(gauss)
10
MA0048
9
2 1.5 1 0.5 0
c(0, 1)
8
Information content
7
c(0, 1)
6
MA0015
5
Position
c(0, 1)
4
Weeder
MA0005
3
2 1.5 1 0.5 0
MA0001
2
2 1.5 1 0.5 0
c(0, 1)
1
Information content
2 1.5 1 0.5 0
c(0, 1)
Information content
Information content
MEME
−501
−401
−301 −201 Position
−101
−1
−501
−401
−301 −201 Position
−101
−1
