Method

Quantifying similarity between motifs

Shobhit Gupta¹ , John A Stamatoyannopoulos¹ , Timothy L Bailey² and William Stafford Noble^1,3

¹Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Box 355065, Seattle, WA 98195, USA

²Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia

³Department of Computer Science and Engineering, University of Washington, 185 Stevens Way, Box 352350, Seattle, WA 98105, USA

author email corresponding author email

Genome Biology 2007, 8:R24doi:10.1186/gb-2007-8-2-r24

Published:	26 February 2007

Subject areas: Bioinformatics, Genetics, Genome studies

Abstract

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.