Research

EXMOTIF: efficient structured motif extraction

Yongqiang Zhang and Mohammed J Zaki

Department of Computer Science, Rensselaer Polytechnic Institute, Troy, New York 12180, USA

author email corresponding author email

Algorithms for Molecular Biology 2006, 1:21doi:10.1186/1748-7188-1-21

Published:	16 November 2006

Abstract

Background

Extracting motifs from sequences is a mainstay of bioinformatics. We look at the problem of mining structured motifs, which allow variable length gaps between simple motif components. We propose an efficient algorithm, called EXMOTIF, that given some sequence(s), and a structured motif template, extracts all frequent structured motifs that have quorum q. Potential applications of our method include the extraction of single/composite regulatory binding sites in DNA sequences.

Results

EXMOTIF is efficient in terms of both time and space and is shown empirically to outperform RISO, a state-of-the-art algorithm. It is also successful in finding potential single/composite transcription factor binding sites.

Conclusion

EXMOTIF is a useful and efficient tool in discovering structured motifs, especially in DNA sequences. The algorithm is available as open-source at: http://www.cs.rpi.edu/~zaki/software/exMotif/ webcite.