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Genome Biol. 2007;8(2):R24.

Quantifying similarity between motifs.

Author information

1
Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Box 355065, Seattle, WA 98195, USA. shobhitg@u.washington.edu

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.

PMID:
17324271
PMCID:
PMC1852410
DOI:
10.1186/gb-2007-8-2-r24
[Indexed for MEDLINE]
Free PMC Article

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