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

 Next Top

Name 

Preview 

Matches 

List 

1_h_k27me3_1_0.743
GCGCGCGCGG
4 RSC30_01_M01520_T,  Rsc30_GR09_U,  RSC30_MA0375.1_J,  Zfp161_primary_SCI09_U
2_h_k27me3_3_0.727
TCGCGGGA
0
3_h_k4me3_2_0.698
CCGACGACCCGG
0
4_h_k4me3_9_0.650
CTTTCGCG
2 SWI4_MA0401.1_J,  E2F_Q3_M00425_T
5_e_k36me3_114_0.395
AAAGTGCTG
0
6_e_k36me3_46_0.398
ACATGGTGAC
0
7_e_k36me3_105_0.398
ATGTTGGCC
0
8_e_k9me3_73_0.400
TAGGCCTCA
0
9_e_k27me3_318_0.578
TAAAAACGAA
2 HOMEZ_01_M01429_T,  Homez_1063.2_Cell08_U
10_e_k27me3_301_0.567
AATACGCGT
0
11_h_k9me3_27_0.437
CCCATGGG
1 GPAM_2_H
12_h_k36me3_1_0.444
TACTTACCTG
2 at_AC_acceptor_SD0001.1_J,  AREB6_01_M00412_T
13_h_k27me3_26_0.554
GAAAGTCG
0
14_h_k36me3_25_0.451
GCACCACATGCA
0
15_e_k27me3_338_0.539
CCCCAAAT
0
16_e_k36me3_181_0.466
GCGCTACCAC
1 SNT2_MA0384.1_J
17_e_k27ac_415_0.534
GTGATTAAA
0
18_h_k9me3_6_0.474
TTGTGATGTGTG
0
19_h_k9me3_8_0.519
GAAGATATTTCC
0
20_h_k36me3_18_0.490
CGGTACCTTT
0

Target Databases

 Previous Next Top

Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 12

Matches to Query: 1_h_k27me3_1_0.743

 Previous Next Top

Summary 

Alignment 

Name RSC30_01_M01520_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.4232e-08
E-value 4.15718e-05
q-value 7.21101e-05
Overlap 10
Offset 6
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name Rsc30_GR09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.48097e-08
E-value 7.24691e-05
q-value 7.21101e-05
Overlap 10
Offset 6
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name RSC30_MA0375.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.53705e-06
E-value 0.0103317
q-value 0.00411222
Overlap 8
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Zfp161_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.30702e-06
E-value 0.0125808
q-value 0.00417283
Overlap 10
Offset 2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 2_h_k27me3_3_0.727

 Previous Next Top

Matches to Query: 3_h_k4me3_2_0.698

 Previous Next Top

Matches to Query: 4_h_k4me3_9_0.650

 Previous Next Top

Summary 

Alignment 

Name SWI4_MA0401.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.88018e-06
E-value 0.020097
q-value 0.0235262
Overlap 7
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name E2F_Q3_M00425_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.07272e-06
E-value 0.0265014
q-value 0.0235262
Overlap 7
Offset -1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 5_e_k36me3_114_0.395

 Previous Next Top

Matches to Query: 6_e_k36me3_46_0.398

 Previous Next Top

Matches to Query: 7_e_k36me3_105_0.398

 Previous Next Top

Matches to Query: 8_e_k9me3_73_0.400

 Previous Next Top

Matches to Query: 9_e_k27me3_318_0.578

 Previous Next Top

Summary 

Alignment 

Name HOMEZ_01_M01429_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.51116e-06
E-value 0.0131771
q-value 0.0147905
Overlap 10
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name Homez_1063.2_Cell08_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.06352e-06
E-value 0.0147905
q-value 0.0147905
Overlap 10
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 10_e_k27me3_301_0.567

 Previous Next Top

Matches to Query: 11_h_k9me3_27_0.437

 Previous Next Top

Summary 

Alignment 

Name GPAM_2_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.16269e-05
E-value 0.0339623
q-value 0.0679246
Overlap 5
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 12_h_k36me3_1_0.444

 Previous Next Top

Summary 

Alignment 

Name at_AC_acceptor_SD0001.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.57341e-12
E-value 1.62799e-08
q-value 3.25599e-08
Overlap 10
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name AREB6_01_M00412_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.07096e-05
E-value 0.0312826
q-value 0.0312826
Overlap 10
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 13_h_k27me3_26_0.554

 Previous Next Top

Matches to Query: 14_h_k36me3_25_0.451

 Previous Next Top

Matches to Query: 15_e_k27me3_338_0.539

 Previous Next Top

Matches to Query: 16_e_k36me3_181_0.466

 Previous Next Top

Summary 

Alignment 

Name SNT2_MA0384.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.64324e-05
E-value 0.0479991
q-value 0.0959981
Overlap 9
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 17_e_k27ac_415_0.534

 Previous Next Top

Matches to Query: 18_h_k9me3_6_0.474

 Previous Next Top

Matches to Query: 19_h_k9me3_8_0.519

 Previous Next Top

Matches to Query: 20_h_k36me3_18_0.490

 Previous Next Top
Previous Next Top
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 54.232 seconds
show model parameters...

Explanation of TOMTOM Results

 Previous Top

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.