Tomtom - Submission form

Data Submission Form

Search one or more DNA motifs against a DNA motif database.

Example Output

Preview

Empty sequence

Preview Error Log

Choose the type of motif

checked> IUPAC Matrix MEME Submitted

Input the motif

Enter a IUPAC DNA motif.

You may use both IUPAC codes and regular expression bracket expressions. For example "NTRGGTCAN" and "[ACGT]T[AG]GGTCA[ACGT]" are equivalent approximations of the example query shown on the right. [close]

Advanced Options

Enter a site count and pseudocount.

sites: pseudocount:

A motif is generated from the specified IUPAC sequence fragment by distributing the site counts equally over each possible residue. The pseudocount is added to each residue in proportion to the background. Thus the total count for a position is the site count plus the pseudocount. For example suppose one of the IUPAC codes entered is 'R'. The IUPAC code 'R' means that both Adenine and Guanine are possible, so with a site count of 10, pseudocount of 1 and a uniform background; the probability of Adenine and Guanine would be:

while the probility of Cytosine and Thymine would be:

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Enter the background model.

A: C: G: T:

The background is used to determine how the pseudocount is distributed. While it is conventional to have the background sum to one these fields will be normalised so you don't have to be exact. You may even use counts instead. [close]

Enter a DNA count/probability matrix.

A matrix is rectangular grid of numbers which shows the relative frequency a nucleotide will occur at a specific position. Two orientations are possible. For example:

Row Matrix

Column Matrix

	A	C	G	T
1	3	8	14	3
2	3	0	0	25
3	19	0	9	0
4	0	1	27	0
5	1	0	26	1
6	0	1	4	23
7	2	23	3	0
8	26	1	0	1
9	5	15	4	4

	1	2	3	4	5	6	7	8	9
A	3	3	19	0	1	0	2	26	5
C	8	0	0	1	0	1	23	1	15
G	14	0	9	27	26	4	3	0	4
T	3	25	0	0	1	23	0	1	4

Click an example to use it as the input.

Tomtom automatically detects the orientation but if for some reason the correct orientation isn't being detected it can be specified in the advanced section. [close]

Advanced Options

Select the orientation.

orientation:

A matrix is column oriented if it has 4 rows and any number of columns. The original Tomtom web format was column oriented. A matrix is row oriented if it has 4 columns and any number of rows. [close]

Enter a site count and pseudocount.

sites: pseudocount:

The site count is only used when a probability matrix is specified, otherwise it is derived from the matrix.
The pseudocount is added to each residue in proportion to the background. Thus the total count for a position is the site count plus the pseudocount. [close]

Enter the background model.

A: C: G: T:

Select a MEME DNA motif file.

By default only the first motif is searched but this can be changed in the advanced section. To search with more than one motif Tomtom must process your request as part of a queue and hence a contact email will be required. See more information on the meme format and the sample MEME DNA motifs. [close]

Advanced Options

Specify which motif(s) to search with.

or all motifs.

The filter supports selecting motifs from the file by their name and/or their order in the file. Any numbers are assumed to refer to the position of the motif in the file. Any other entry is assumed to be a motif name (or ID). Motif names can not start with a dash and can only contain alphanumeric characters plus : _ . and -. The motifs should be separated by spaces. [close]

Tomtom will use the submitted motifs.

Choose the motif database to search

Tomtom can search databases installed on the server or search a user uploaded database in MEME DNA motif format by selecting the "Upload Your Own Database" option. Uploaded databases are searched in a queue and so require an email address. For more information browse the supported databases. [close]

Input the database

Select a MEME motif database file.

An uploaded database is a normal MEME DNA motif file with lots of motifs. The uploaded database must be smaller than 5MB. [close]

Input job queue details

Enter your email address.

Re-enter your email address.

The email is used to notify you of your results but is not stored. [close]

Optionally enter a job description.

The job description will be included in the notification email you receive. [close]

Advanced Options

Select the motif column comparison function

Motifs are compared column by column. In the following equations X is the set of probabilities from one column and Y the probabilities from the compared column. The subscript a refers to the letter from the nucleotide alphabet A.

Pearson correlation coefficient
Euclidean distance
Sandelin-Wasserman similarity

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Set the significance threshold

There are two ways of specifying the threshold.

E-value: The expected number of false positives. This may be any positive number.
q-value: Minimum False Discovery Rate at which a result is declared significant. This is a number between zero and one non-inclusive.

[close]

Activate complete scoring

complete scoring

Complete scoring takes into account unaligned columns in the calculation of scores. It is recommended that you leave this feature enabled unless you are trying to recreate old results. [close]

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