Tomtom is a tool for comparing a DNA motif to a database of known motifs. For an in-depth explanation of the Tomtom software see here.

Recommended Settings

We recommend most users use the Tomtom defaults of q-value for score, the cutoff of 0.5 and the Pearson correlation coefficent for distance metric.

Parameters

We offer users the options of choosing which distance metric can be used to find matching motifs. Specifically, we offer the Pearson correlation coefficient, the Euclidean distance and the Sandelin-Wasserman Function.

• The Pearson correlation coefficient measures the similarity between columns of position weight matrices (PWMs).
• The Euclidean distance can be thought of as the length of the straight line between two PWMs.
• The Sandelin-Wasserman function sums the column-wise differences between PWMs.

We also offer the choice of E-value and q-value to threshold the results returned by Tomtom.

• The E-value controls the expected number of false positives and can be any number.
• The q-value controls the false discovery rate and is a number between 0 and 1.

Note that at this time we only offer Tomtom output in txt format.

Citation

If you use this tool, please cite: Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs", Genome Biology, 8(2):R24, 2007.