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_k36me3-h1_0.655
GCCTCCCAAG
1 IK_Q5_M01169_T
2_e_k36me3-h1_0.653
GGAGTTCGAGACC
2 RPC155_01_M01798_T,  BDP1_01_M01796_T
3_h_k36me3-h1_0.650
CCCGGCTAAT
1 MTHFD1_5_H
4_e_k36me3-h1_0.648
CACCACGCCCG
0
5_h_k36me3-h1_0.648
GTAGAGACGG
0
6_e_k36me3-h1_0.647
GGGATTACA
1 PITX2_Q2_M00482_T
7_h_k36me3-h1_0.636
GGCAGGAGAT
0
8_e_k36me3-h1_0.633
TGGCTCATGCC
0
9_h_k36me3-h1_0.631
GTTTCACCGT
0
10_h_k36me3-h1_0.631
GATCGCGCCA
0
11_e_k36me3-h1_0.627
CCCGAGTAG
0
12_e_k36me3-h1_0.624
ACTGCACTC
0
13_e_k36me3-h1_0.623
CCCGGGAGG
0
14_e_k36me3-h1_0.615
CCCGGCCAA
0
15_e_k36me3-h1_0.614
AACCTCTGC
0
16_e_k36me3-h1_0.613
GATCTGCCC
0
17_h_k36me3-h1_0.612
GCGAATCG
0
18_h_k36me3-h1_0.592
GTTAGTAG
0
19_e_k36me3-h1_0.589
ACGCGGCGC
1 ODC1_3_H
20_e_k36me3-h1_0.587
GACAGAGTCT
0
21_e_k36me3-h1_0.585
CTGAGGTCA
2 TERALPHA_Q6_M01724_T,  T3R_01_M00239_T
22_e_k36me3-h1_0.582
AGGTGGGCG
0
23_e_k36me3-h1_0.581
AGGTGTGAG
2 TBX5_Q5_M01044_T,  TBR2_01_M01774_T
24_e_k36me3-msc_0.579
AGCAGCAGC
0
25_e_k36me3-h1_0.574
CATGCCCAG
0
26_h_k36me3-msc_0.564
TGCTGCATGAAG
0
27_e_k36me3-h1_0.561
TAAGACGGA
0
28_e_k36me3-msc_0.549
GTGTTCACA
0
29_e_k36me3-msc_0.546
ACACCTTCC
0
30_e_k36me3-h1_0.540
ATGGTGGTGT
1 ING4_01_M01743_T

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 11

Matches to Query: 1_e_k36me3-h1_0.655

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Summary 

Alignment 

Name IK_Q5_M01169_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.70392e-06
E-value 0.00497714
q-value 0.00995428
Overlap 10
Offset 0
Orientation Reverse Complement
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Matches to Query: 2_e_k36me3-h1_0.653

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Summary 

Alignment 

Name RPC155_01_M01798_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.79908e-08
E-value 5.25511e-05
q-value 0.000105102
Overlap 13
Offset 3
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name BDP1_01_M01796_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.43162e-06
E-value 0.0129447
q-value 0.0129447
Overlap 12
Offset -1
Orientation Reverse Complement
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Matches to Query: 3_h_k36me3-h1_0.650

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Summary 

Alignment 

Name MTHFD1_5_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.53952e-05
E-value 0.0449694
q-value 0.0899388
Overlap 6
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 4_e_k36me3-h1_0.648

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Matches to Query: 5_h_k36me3-h1_0.648

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Matches to Query: 6_e_k36me3-h1_0.647

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Summary 

Alignment 

Name PITX2_Q2_M00482_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.99697e-06
E-value 0.0233591
q-value 0.0467183
Overlap 9
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 7_h_k36me3-h1_0.636

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Matches to Query: 8_e_k36me3-h1_0.633

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Matches to Query: 9_h_k36me3-h1_0.631

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Matches to Query: 10_h_k36me3-h1_0.631

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Matches to Query: 11_e_k36me3-h1_0.627

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Matches to Query: 12_e_k36me3-h1_0.624

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Matches to Query: 13_e_k36me3-h1_0.623

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Matches to Query: 14_e_k36me3-h1_0.615

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Matches to Query: 15_e_k36me3-h1_0.614

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Matches to Query: 16_e_k36me3-h1_0.613

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Matches to Query: 17_h_k36me3-h1_0.612

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Matches to Query: 18_h_k36me3-h1_0.592

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Matches to Query: 19_e_k36me3-h1_0.589

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Summary 

Alignment 

Name ODC1_3_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.29548e-05
E-value 0.0378411
q-value 0.0429767
Overlap 6
Offset -2
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 20_e_k36me3-h1_0.587

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Matches to Query: 21_e_k36me3-h1_0.585

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Summary 

Alignment 

Name TERALPHA_Q6_M01724_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.64593e-06
E-value 0.0106498
q-value 0.0142457
Overlap 9
Offset 1
Orientation Normal
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Summary 

Alignment 

Name T3R_01_M00239_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.94503e-06
E-value 0.0144444
q-value 0.0142457
Overlap 9
Offset 2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 22_e_k36me3-h1_0.582

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Matches to Query: 23_e_k36me3-h1_0.581

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Summary 

Alignment 

Name TBX5_Q5_M01044_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.82622e-08
E-value 5.33439e-05
q-value 0.000106655
Overlap 9
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name TBR2_01_M01774_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.14116e-06
E-value 0.0237803
q-value 0.023773
Overlap 9
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 24_e_k36me3-msc_0.579

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Matches to Query: 25_e_k36me3-h1_0.574

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Matches to Query: 26_h_k36me3-msc_0.564

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Matches to Query: 27_e_k36me3-h1_0.561

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Matches to Query: 28_e_k36me3-msc_0.549

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Matches to Query: 29_e_k36me3-msc_0.546

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Matches to Query: 30_e_k36me3-h1_0.540

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Summary 

Alignment 

Name ING4_01_M01743_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.00395e-06
E-value 0.00877455
q-value 0.0175491
Overlap 6
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]
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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 78.329 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.