TOMTOM

Name	Preview	Matches	List
1_e_0_0.753	CGCCTGTAATC	0
2_e_13_0.748	CTGTAATCCC	0
3_e_5_0.740	ATCACTTGAG	1	tin_MA0247.1_J
4_e_3_0.739	TTTTTAGTAGAG	0
5_e_4_0.739	AGGAGTTCGAG	1	RPC155_01_M01798_T
6_e_21_0.736	GTCTCGAACT	1	RPC155_01_M01798_T
7_e_43_0.733	CTGGGCAACA	0
8_e_42_0.728	GCCTCCCAA	1	IK_Q5_M01169_T
9_e_45_0.727	CCAGCCTGGCC	0
10_e_32_0.711	AAATTAGCCA	0
11_e_49_0.711	AGGCTGAGG	0
12_e_68_0.708	CAGCACTTTG	0
13_e_37_0.707	GGGTTTCAC	0
14_e_6_0.703	ATCGTGCCAC	0
15_e_89_0.697	ATCCCAGCA	0
16_e_16_0.694	CCGAGTAGC	0
17_e_30_0.678	AAATACAAA	0
18_e_66_0.651	ACAGAGCGAG	0
19_e_124_0.612	GCATGTGCC	0
20_e_283_0.546	ATGATCACG	0

Database	Number of Motifs	Motifs Matched
trnsfcJsprUnprobHpdiCmbned3.meme	2921	3

Database

Number of Motifs

Motifs Matched

trnsfcJsprUnprobHpdiCmbned3.meme

2921

Name

tin_MA0247.1_J

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.48567e-05

E-value

0.0433963

q-value

0.0867926

Overlap

Offset

-2

Orientation

Reverse Complement

Name

RPC155_01_M01798_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

2.07339e-07

E-value

0.000605638

q-value

0.00121128

Overlap

Offset

Orientation

Normal

Name

RPC155_01_M01798_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.02934e-05

E-value

0.030067

q-value

0.0601341

Overlap

Offset

Orientation

Reverse Complement

Name

IK_Q5_M01169_T

Database

trnsfcJsprUnprobHpdiCmbned3.meme

p-value

1.72336e-06

E-value

0.00503393

q-value

0.0100679

Overlap

Offset

Orientation

Reverse Complement

The TOMTOM results consist of

The query motifs with links to further information on matches. [View]
The target databases with information on the number of matches. [View]
The matches between query motifs and target motifs. [View]
- The summary of match information.
- An alignment of the two motifs.
The program details including:
1. The version of TOMTOM and the date it was released. [View]
2. The reference to cite if you use TOMTOM in your research. [View]
3. The command line summary detailing the parameters with which you ran TOMTOM. [View]
This explanation of how to interpret TOMTOM results.

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.

Query Motifs

Name

Preview

Matches

List

Target Databases

Database

Number of Motifs

Motifs Matched

Matches to Query: 1_e_0_0.753

Matches to Query: 2_e_13_0.748

Matches to Query: 3_e_5_0.740

Summary

Alignment

Matches to Query: 4_e_3_0.739

Matches to Query: 5_e_4_0.739

Summary

Alignment

Matches to Query: 6_e_21_0.736

Summary

Alignment

Matches to Query: 7_e_43_0.733

Matches to Query: 8_e_42_0.728

Summary

Alignment

Matches to Query: 9_e_45_0.727

Matches to Query: 10_e_32_0.711

Matches to Query: 11_e_49_0.711

Matches to Query: 12_e_68_0.708

Matches to Query: 13_e_37_0.707

Matches to Query: 14_e_6_0.703

Matches to Query: 15_e_89_0.697

Matches to Query: 16_e_16_0.694

Matches to Query: 17_e_30_0.678

Matches to Query: 18_e_66_0.651

Matches to Query: 19_e_124_0.612

Matches to Query: 20_e_283_0.546

TOMTOM version

Reference

Command line summary

Model parameters

Explanation of TOMTOM Results

The TOMTOM results consist of

Inputs

Query Motifs

Target Databases

Matches

Summary Table

Alignment

Create custom LOGO