Quantifying similarity between motifs
Shobhit Gupta, John A. Stamatoyannopoulos, Timothy L. Bailey and William Stafford Noble
Genome Biology. 8:R24, 2007.
Abstract
A common question in the context of de novo motif discovery is whether a newly discovered, putative motif resembles any previously discovered motif in an existing database. To answer this question, we define a statistical measure of motif-motif similarity, and we describe an algorithm, called Tomtom, for searching a database of motifs with a given query motif. Experimental simulations demonstrate the accuracy of Tomtom's E-values and its effectiveness in finding similar motifs.
Online supplement
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