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_h_1_0.826
CGCGCATA
0
2_e_2_0.799
CCGCCGCCG
1 ERF2_01_M01057_T
3_h_5_0.751
GCGGAGAA
1 PDR8_01_M01613_T
4_h_8_0.749
TTCGATCG
0
5_h_7_0.736
CGACGATT
1 MSRA_2_H
6_h_4_0.732
TTTCCCCCTCGC
2 MZF1_02_M00084_T,  MZF1_5-13_MA0057.1_J
7_re_76_0.281
AGCACAGTGC
0
8_re_108_0.315
CACAGCTGCA
3 NEUROD_01_M01287_T,  NEUROD_02_M01288_T,  LBP1_Q6_M00644_T
9_e_76_0.684
CTCGCCTTC
0
10_re_63_0.320
GCCTGGCAC
0
11_e_159_0.667
AGCCGAGGC
0
12_e_174_0.665
CGGGTTCCC
0
13_re_107_0.337
CAAGGTCAC
5 NR4A2_MA0160.1_J,  ERR2_01_M01589_T,  SF1_Q6_M00727_T,  GTF3C5_2_H,  DAX1_01_M01248_T
14_e_318_0.657
CCTTTTAAA
0
15_re_70_0.348
CTGTGTGTC
0
16_re_134_0.350
ACAGCACGTG
0
17_e_333_0.639
AATACCGTA
0
18_e_272_0.637
CACGGAAAT
4 YRM1_MA0438.1_J,  YRM1_01_M01501_T,  Yrm1_GR09_U,  YKL222C_MA0428.1_J
19_e_233_0.568
CAAACCCCA
0
20_e_292_0.560
AAAGGAGTG
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 17

Matches to Query: 1_h_1_0.826

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Matches to Query: 2_e_2_0.799

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Summary 

Alignment 

Name ERF2_01_M01057_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.54414e-07
E-value 0.00103524
q-value 0.00205524
Overlap 7
Offset -1
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 3_h_5_0.751

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Summary 

Alignment 

Name PDR8_01_M01613_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.85013e-06
E-value 0.0200092
q-value 0.0399855
Overlap 7
Offset 0
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 4_h_8_0.749

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Matches to Query: 5_h_7_0.736

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Summary 

Alignment 

Name MSRA_2_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.5912e-06
E-value 0.0280159
q-value 0.0560318
Overlap 6
Offset -1
Orientation Normal
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Matches to Query: 6_h_4_0.732

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Summary 

Alignment 

Name MZF1_02_M00084_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.34199e-06
E-value 0.00976195
q-value 0.0194675
Overlap 11
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name MZF1_5-13_MA0057.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.64657e-05
E-value 0.0480963
q-value 0.0479574
Overlap 10
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 7_re_76_0.281

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Matches to Query: 8_re_108_0.315

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Summary 

Alignment 

Name NEUROD_01_M01287_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.73415e-06
E-value 0.0167494
q-value 0.0166434
Overlap 6
Offset -2
Orientation Normal
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Summary 

Alignment 

Name NEUROD_02_M01288_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.96983e-06
E-value 0.0291219
q-value 0.0192917
Overlap 10
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name LBP1_Q6_M00644_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.43078e-05
E-value 0.041793
q-value 0.0207643
Overlap 7
Offset -2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 9_e_76_0.684

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Matches to Query: 10_re_63_0.320

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Matches to Query: 11_e_159_0.667

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Matches to Query: 12_e_174_0.665

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Matches to Query: 13_re_107_0.337

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Summary 

Alignment 

Name NR4A2_MA0160.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.60125e-07
E-value 0.00222032
q-value 0.00239148
Overlap 8
Offset -1
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name ERR2_01_M01589_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.2422e-07
E-value 0.00240755
q-value 0.00239148
Overlap 9
Offset 1
Orientation Normal
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Summary 

Alignment 

Name SF1_Q6_M00727_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.61798e-06
E-value 0.0134891
q-value 0.00893274
Overlap 8
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name GTF3C5_2_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.01195e-05
E-value 0.0295591
q-value 0.0146809
Overlap 6
Offset -3
Orientation Reverse Complement
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Summary 

Alignment 

Name DAX1_01_M01248_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.41971e-05
E-value 0.0414698
q-value 0.0164772
Overlap 9
Offset 6
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 14_e_318_0.657

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Matches to Query: 15_re_70_0.348

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Matches to Query: 16_re_134_0.350

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Matches to Query: 17_e_333_0.639

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Matches to Query: 18_e_272_0.637

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Summary 

Alignment 

Name YRM1_MA0438.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.91045e-07
E-value 0.00114224
q-value 0.00226845
Overlap 8
Offset -1
Orientation Normal
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Summary 

Alignment 

Name YRM1_01_M01501_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.07179e-05
E-value 0.031307
q-value 0.0167528
Overlap 9
Offset 4
Orientation Normal
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Summary 

Alignment 

Name Yrm1_GR09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.07179e-05
E-value 0.031307
q-value 0.0167528
Overlap 9
Offset 4
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name YKL222C_MA0428.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.15516e-05
E-value 0.0337423
q-value 0.0167528
Overlap 9
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 19_e_233_0.568

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Matches to Query: 20_e_292_0.560

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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 44.128 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.