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Quantifying similarity between motifs.

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.

SUBMITTER: Gupta S 

PROVIDER: S-EPMC1852410 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature

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Quantifying similarity between motifs.

Gupta Shobhit S   Stamatoyannopoulos John A JA   Bailey Timothy L TL   Noble William Stafford WS  

Genome biology 20070101 2

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. ...[more]