Tomtom - Submission form

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Tomtom will compare each of the query motifs to each of the target motifs.

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Tomtom will compare each of the query motifs to each of the target motifs.

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When this option is selected the Tomtom search is submitted to a special queue so that it can (hopefully) be run immediately. Only Tomtom jobs are submitted to this queue, and only the first motif in your input will be used as the query. This restriction helps ensure that these special Tomtom jobs will usually run very quickly after you submit them.

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Select the motif comparison function.

- Pearson Correlation Coefficient - The Pearson correlation coefficient between the aligned columns of the query and target motif, maximized over all alignments of the two motifs.
- Euclidean Distance - The sum of the Euclidean distance between aligned columns of the query and target motif, minimized over all alignments of the two motifs.
- Sandelin-Wasserman Similarity - The similarity function defined in Sandelin A, Wasserman WW, "Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics", J Mol Biol., 2004, 338:207-215, maximized over all alignments of the two motifs.

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Only matches with a significance (select E-value or q-value on the left) less than or equal to the value (given on the right) will be reported.

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If selected, even unaligned columns in the target and query motifs are used in computing the comparison function. Otherwise, only the aligned columns are considered in computing the comparison function.

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If selected, only the target motifs as given are compared with the query motif. Otherwise, both the target motif and its reverse complement are compared with the query (for complementable alphabets).

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Tomtom - Motif Comparison Tool
../doc/images/tomtom_icon.png: Tomtom Logo

Data Submission Form

Search one or more motifs against a motif database.

query_motifs query motifs Input query motifs Enter the motif(s) to compare to known motifs. TEXT register_component
Example Output
target_motifs target motifs Select target motifs Select a motif database or provide motifs to compare with. DATABASE register_component

## Run immediately

Search with one motif (faster queue)

### Select the motif column comparison function

### Set the significance threshold

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### Activate complete scoring

complete scoring

### Scoring reverse complement motifs

Do not score the reverse complements of target motifs