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_re_32_0.401
GGCCTCCCA
0
2_re_54_0.403
GCAGGAGAATCGC
0
3_re_93_0.408
AATCCCAGC
0
4_re_45_0.410
CCCCGTCTC
0
5_re_95_0.411
CGAGGTTGCAG
0
6_re_100_0.413
GTATTTTTAGTA
2 MEF2C_01_M01773_T,  MEF2_04_M00233_T
7_re_72_0.416
CAGCTACTCT
0
8_re_21_0.419
AAACCCCGT
0
9_re_124_0.420
CTCACTGCA
0
10_re_139_0.424
AAAAAAAAA
1 Srf_secondary_SCI09_U
11_re_0_0.426
AAAATTAGCC
0
12_re_46_0.427
GGCGACAGAG
0
13_re_153_0.428
AGGCGCCTG
0
14_re_65_0.429
GAGACCAGC
0
15_e_69_0.436
CCGACGACG
0
16_re_208_0.453
TAAAATACGT
0
17_e_112_0.544
GAGAATTCA
0
18_e_91_0.542
CAGATTCTA
0
19_e_185_0.537
GAACCTTTC
0
20_e_232_0.536
ATTCCAGAA
1 HNRPH3_9_H
21_e_72_0.535
ATAGAGCAGG
0
22_e_87_0.535
CATTCATAG
0
23_h_23_0.468
CGATGACG
2 VJUN_01_M00036_T,  Jundm2_primary_SCI09_U
24_e_199_0.532
ATGCACACA
0
25_e_198_0.532
CACATTACA
0
26_e_85_0.530
AAGGAATCA
0
27_re_176_0.474
GTGGTGCAT
0
28_h_8_0.525
GAAGATATTCCC
0
29_e_73_0.522
TCGAAAGC
0
30_e_86_0.508
GCGCTTTGA
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 6

Matches to Query: 1_re_32_0.401

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Matches to Query: 2_re_54_0.403

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Matches to Query: 3_re_93_0.408

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Matches to Query: 4_re_45_0.410

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Matches to Query: 5_re_95_0.411

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Matches to Query: 6_re_100_0.413

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Summary 

Alignment 

Name MEF2C_01_M01773_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.15488e-06
E-value 0.0062944
q-value 0.0125888
Overlap 12
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name MEF2_04_M00233_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.49655e-05
E-value 0.0437143
q-value 0.0437143
Overlap 12
Offset 5
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 7_re_72_0.416

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Matches to Query: 8_re_21_0.419

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Matches to Query: 9_re_124_0.420

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Matches to Query: 10_re_139_0.424

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Summary 

Alignment 

Name Srf_secondary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.93295e-06
E-value 0.0144091
q-value 0.0288183
Overlap 9
Offset 4
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 11_re_0_0.426

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Matches to Query: 12_re_46_0.427

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Matches to Query: 13_re_153_0.428

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Matches to Query: 14_re_65_0.429

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Matches to Query: 15_e_69_0.436

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Matches to Query: 16_re_208_0.453

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Matches to Query: 17_e_112_0.544

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Matches to Query: 18_e_91_0.542

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Matches to Query: 19_e_185_0.537

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Matches to Query: 20_e_232_0.536

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Summary 

Alignment 

Name HNRPH3_9_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.20938e-05
E-value 0.0353259
q-value 0.0704841
Overlap 6
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 21_e_72_0.535

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Matches to Query: 22_e_87_0.535

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Matches to Query: 23_h_23_0.468

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Summary 

Alignment 

Name VJUN_01_M00036_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.55767e-06
E-value 0.0249969
q-value 0.0358713
Overlap 8
Offset 1
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name Jundm2_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.5972e-05
E-value 0.0466543
q-value 0.0358713
Overlap 8
Offset 1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 24_e_199_0.532

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Matches to Query: 25_e_198_0.532

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Matches to Query: 26_e_85_0.530

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Matches to Query: 27_re_176_0.474

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Matches to Query: 28_h_8_0.525

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Matches to Query: 29_e_73_0.522

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Matches to Query: 30_e_86_0.508

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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 76.385 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.