Quantifying similarity between motifs
1 Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Box 355065, Seattle, WA 98195, USA
2 Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
3 Department of Computer Science and Engineering, University of Washington, 185 Stevens Way, Box 352350, Seattle, WA 98105, USA
Genome Biology 2007, 8:R24 doi:10.1186/gb-2007-8-2-r24Published: 26 February 2007
A common question within 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.