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PairMotif: A New Pattern-Driven Algorithm for Planted (l, d) DNA Motif Search

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  • Qiang Yu
  • Hongwei Huo
  • Yipu Zhang
  • Hongzhi Guo

Abstract

Motif search is a fundamental problem in bioinformatics with an important application in locating transcription factor binding sites (TFBSs) in DNA sequences. The exact algorithms can report all (l, d) motifs and find the best one under a specific objective function. However, it is still a challenging task to identify weak motifs, since either a large amount of memory or execution time is required by current exact algorithms. A new exact algorithm, PairMotif, is proposed for planted (l, d) motif search (PMS) in this paper. To effectively reduce both candidate motifs and scanned l-mers, multiple pairs of l-mers with relatively large distances are selected from input sequences to restrict the search space. Comparisons with several recently proposed algorithms show that PairMotif requires less storage space and runs faster on most PMS instances. Particularly, among the algorithms compared, only PairMotif can solve the weak instance (27, 9) within 10 hours. Moreover, the performance of PairMotif is stable over the sequence length, which allows it to identify motifs in longer sequences. For the real biological data, experimental results demonstrate the validity of the proposed algorithm.

Suggested Citation

  • Qiang Yu & Hongwei Huo & Yipu Zhang & Hongzhi Guo, 2012. "PairMotif: A New Pattern-Driven Algorithm for Planted (l, d) DNA Motif Search," PLOS ONE, Public Library of Science, vol. 7(10), pages 1-10, October.
    • Handle: RePEc:plo:pone00:0048442
    DOI: 10.1371/journal.pone.0048442
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    References listed on IDEAS

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    1. Andrew K Miller & Cristin G Print & Poul M F Nielsen & Edmund J Crampin, 2010. "A Bayesian Search for Transcriptional Motifs," PLOS ONE, Public Library of Science, vol. 5(11), pages 1-7, November.
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    Cited by:

    1. Haitao Guo & Hongwei Huo & Qiang Yu, 2016. "SMCis: An Effective Algorithm for Discovery of Cis-Regulatory Modules," PLOS ONE, Public Library of Science, vol. 11(9), pages 1-17, September.

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