Quantifying similarity between motifs

Genome Biol. 2007;8(2):R24. doi: 10.1186/gb-2007-8-2-r24.


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.

MeSH terms

  • Algorithms*
  • Amino Acid Motifs / genetics*
  • Computational Biology / methods*
  • Databases, Genetic*
  • Sequence Homology*
  • Software*