EXMOTIF

Efficient structured motif extraction

Yongqiang Zhang, Mohammed J. Zaki

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

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. EXMOTIF is efficient in terms of both time and space and outperforms RISO, a state-of-the-art algorithm.

Original languageEnglish
Title of host publicationProceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining
PublisherAssociation for Computing Machinery
Pages32-41
Number of pages10
Publication statusPublished - 1 Jan 2006
Externally publishedYes
Event6th International Workshop on Data Mining in Bioinformatics, BIOKDD 2006 - Held in Conjunction with 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, KDD 2006 - Philadelphia, United States
Duration: 20 Aug 2006 → …

Other

Other6th International Workshop on Data Mining in Bioinformatics, BIOKDD 2006 - Held in Conjunction with 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, KDD 2006
CountryUnited States
CityPhiladelphia
Period20/8/06 → …

Fingerprint

DNA sequences
Binding sites
Bioinformatics
Composite materials

ASJC Scopus subject areas

  • Software
  • Information Systems

Cite this

Zhang, Y., & Zaki, M. J. (2006). EXMOTIF: Efficient structured motif extraction. In Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (pp. 32-41). Association for Computing Machinery.

EXMOTIF : Efficient structured motif extraction. / Zhang, Yongqiang; Zaki, Mohammed J.

Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. Association for Computing Machinery, 2006. p. 32-41.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Zhang, Y & Zaki, MJ 2006, EXMOTIF: Efficient structured motif extraction. in Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. Association for Computing Machinery, pp. 32-41, 6th International Workshop on Data Mining in Bioinformatics, BIOKDD 2006 - Held in Conjunction with 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, KDD 2006, Philadelphia, United States, 20/8/06.
Zhang Y, Zaki MJ. EXMOTIF: Efficient structured motif extraction. In Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. Association for Computing Machinery. 2006. p. 32-41
Zhang, Yongqiang ; Zaki, Mohammed J. / EXMOTIF : Efficient structured motif extraction. Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. Association for Computing Machinery, 2006. pp. 32-41
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