TOol for Motif TO Motif comparison (TOMTOM)

For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net.

If you use TOMTOM in your research, please cite the following paper:
Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs", Genome Biology, 8(2):R24, 2007.

Query Motifs  |  Target Databases  |  Matches  |  Program information  |  Explanation

Query Motifs

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Name 

Preview 

Matches 

List 

1_e_3_0.743
CCGCGCGCC
1 ZF5_01_M00716_T
2_e_51_0.630
GCGGGCTCC
0
3_h_7_0.630
AAACGCGC
0
4_e_20_0.628
GCGCGCACA
0
5_e_115_0.596
CGCCTACGA
0
6_e_68_0.593
CGTCTCCCG
0
7_re_1_0.416
CACGTGGCCT
15 PIF3_02_M00435_T,  PIF3_01_M00434_T,  ABF1_02_M00400_T,  GBF_Q2_M00441_T,  CBF1_02_M01699_T,  CG1_Q6_M00440_T,  CMYC_02_M01154_T,  GBP_Q6_M00182_T,  USF1_MA0093.1_J,  ABF_Q2_M00442_T
8_re_11_0.417
AGCTGTGTG
0
9_re_70_0.418
CAGCCCTGCC
0
10_e_190_0.582
CACCGTGGTG
0
11_re_5_0.419
CTCTGTGCCT
0
12_re_91_0.436
CAGATGAGGT
0
13_e_130_0.563
CGGGAGGGA
0
14_h_12_0.559
TTCGCGGAAA
0
15_re_71_0.452
CTCTGCCACA
0
16_e_169_0.541
ATTACG
0
17_e_305_0.520
AGACGTTTA
0
18_h_10_0.511
GCTTGCAAAA
0
19_h_23_0.504
ATGCATTT
0
20_e_332_0.504
AAATGACC
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 16

Matches to Query: 1_e_3_0.743

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Summary 

Alignment 

Name ZF5_01_M00716_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.6186e-06
E-value 0.0193329
q-value 0.0384345
Overlap 8
Offset 0
Orientation Reverse Complement
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Matches to Query: 2_e_51_0.630

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Matches to Query: 3_h_7_0.630

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Matches to Query: 4_e_20_0.628

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Matches to Query: 5_e_115_0.596

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Matches to Query: 6_e_68_0.593

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Matches to Query: 7_re_1_0.416

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Summary 

Alignment 

Name PIF3_02_M00435_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.3352e-06
E-value 0.00390012
q-value 0.00323409
Overlap 10
Offset 6
Orientation Reverse Complement
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Summary 

Alignment 

Name PIF3_01_M00434_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.69426e-06
E-value 0.00494894
q-value 0.00323409
Overlap 10
Offset 6
Orientation Reverse Complement
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Summary 

Alignment 

Name ABF1_02_M00400_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.80429e-06
E-value 0.00527033
q-value 0.00323409
Overlap 10
Offset 10
Orientation Normal
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Summary 

Alignment 

Name GBF_Q2_M00441_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.29728e-06
E-value 0.00671037
q-value 0.00323409
Overlap 9
Offset 3
Orientation Normal
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Summary 

Alignment 

Name CBF1_02_M01699_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.01926e-06
E-value 0.00881925
q-value 0.00340038
Overlap 6
Offset 0
Orientation Normal
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Summary 

Alignment 

Name CG1_Q6_M00440_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.31591e-06
E-value 0.0184488
q-value 0.00492099
Overlap 9
Offset 2
Orientation Normal
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Summary 

Alignment 

Name CMYC_02_M01154_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.81338e-06
E-value 0.0257439
q-value 0.00492099
Overlap 9
Offset 3
Orientation Normal
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Summary 

Alignment 

Name GBP_Q6_M00182_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.63365e-06
E-value 0.0281399
q-value 0.00492099
Overlap 9
Offset 3
Orientation Reverse Complement
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Summary 

Alignment 

Name USF1_MA0093.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.19975e-05
E-value 0.0350446
q-value 0.00492099
Overlap 7
Offset 0
Orientation Normal
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Summary 

Alignment 

Name ABF_Q2_M00442_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.24083e-05
E-value 0.0362448
q-value 0.00492099
Overlap 10
Offset 5
Orientation Normal
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Summary 

Alignment 

Name EMBP1_Q2_M00366_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.31359e-05
E-value 0.0383699
q-value 0.00492099
Overlap 8
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name USF_01_M00121_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.38083e-05
E-value 0.0403341
q-value 0.00492099
Overlap 10
Offset 4
Orientation Normal
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Summary 

Alignment 

Name Mycn_MA0104.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.4289e-05
E-value 0.0417383
q-value 0.00492099
Overlap 8
Offset 2
Orientation Normal
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Summary 

Alignment 

Name Arnt_MA0004.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.66329e-05
E-value 0.0485848
q-value 0.00492962
Overlap 6
Offset 0
Orientation Normal
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Summary 

Alignment 

Name Mycn_MA0104.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.66329e-05
E-value 0.0485848
q-value 0.00492962
Overlap 6
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 8_re_11_0.417

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Matches to Query: 9_re_70_0.418

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Matches to Query: 10_e_190_0.582

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Matches to Query: 11_re_5_0.419

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Matches to Query: 12_re_91_0.436

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Matches to Query: 13_e_130_0.563

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Matches to Query: 14_h_12_0.559

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Matches to Query: 15_re_71_0.452

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Matches to Query: 16_e_169_0.541

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Matches to Query: 17_e_305_0.520

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Matches to Query: 18_h_10_0.511

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Matches to Query: 19_h_23_0.504

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Matches to Query: 20_e_332_0.504

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TOMTOM version
4.8.1 (Release date: Tue Feb 7 14:03:40 EST 2012)
Reference
Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs", Genome Biology, 8(2):R24, 2007.
Command line summary

Background letter frequencies (from first motif database):
A: 0.295   C: 0.205   G: 0.205   T: 0.295

Result calculation took 45.461 seconds
show model parameters...

Explanation of TOMTOM Results

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The TOMTOM results consist of

Inputs

The important inputs to TOMTOM.

Query Motifs

The query motifs section lists the motifs that were searched for in the target databases as well as links to matches found.

Name
The motif name.
Alt. Name
The alternative motif name. This column may be hidden if no query motifs have an alternate name.
Website
A link to a website which has more information on the motif. This column may be hidden if no query motifs have website information.
Preview
The motif preview. On supporting browsers this will display as a motif logo, otherwise the consensus sequence will be displayed.
Matches
The number of significant matches.
List
Links to the first 20 matches
Target Databases

The target motifs section lists details on the motif databases that were specifed to search.

Database
The database name.
Number of Motifs
The number of motifs read from the motif database minus the number that had to be discarded due to conflicting ids.
Motifs Matched
The number of motifs that had a match with at least one of the query motifs.

Matches

The matches section list the group of motifs that match each query motif. For each query-target match the following information is given:

Summary Table

The summary gives the important statistics about the motif match.

Name
The name of the matched motif.
Alt. Name
The alternative name of the matched motif.
p-value
The probability that the match occurred by random chance according to the null model.
E-value
The expected number of false positives in the matches up to this point.
q-value
The minimum False Discovery Rate required to include the match.
Overlap
The number of letters that overlaped in the optimal alignment.
Offset
The offset of the query motif to the matched motif in the optimal alignment.
Orientation
The orientation of the matched motif that gave the optimal alignment. A value of "normal" means that the matched motif is as it appears in the database otherwise the matched motif has been reverse complemented.
Alignment

The image shows the alignment of the two motifs. The matched motif is shown on the top and the query motif is shown on the bottom.

Create custom LOGO

By clicking the link "Create custom LOGO ↧" a form to make custom logos will be displayed. The download button can then be clicked to generate a motif matching the selected specifications.

Image Type
Two image formats, png and eps, are avaliable. The pixel based portable network graphic (png) format is commonly used on the Internet and the Encapsulated PostScript (eps) format is more suitable for publications that might require scaling.
Error bars
Toggle error bars indicating the confidence of a motif based on the number of sites used in its creation.
SSC
Toggle adding pseudocounts for Small Sample Correction.
Flip
Toggle a full reverse complement of the alignment.
Width
Specify the width of the generated motif.
Height
Specify the height of the generated motif.