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AMD, an Automated Motif Discovery Tool Using Stepwise Refinement of Gapped Consensuses

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  • Jiantao Shi
  • Wentao Yang
  • Mingjie Chen
  • Yanzhi Du
  • Ji Zhang
  • Kankan Wang

Abstract

Motif discovery is essential for deciphering regulatory codes from high throughput genomic data, such as those from ChIP-chip/seq experiments. However, there remains a lack of effective and efficient methods for the identification of long and gapped motifs in many relevant tools reported to date. We describe here an automated tool that allows for de novo discovery of transcription factor binding sites, regardless of whether the motifs are long or short, gapped or contiguous.

Suggested Citation

  • Jiantao Shi & Wentao Yang & Mingjie Chen & Yanzhi Du & Ji Zhang & Kankan Wang, 2011. "AMD, an Automated Motif Discovery Tool Using Stepwise Refinement of Gapped Consensuses," PLOS ONE, Public Library of Science, vol. 6(9), pages 1-10, September.
    • Handle: RePEc:plo:pone00:0024576
    DOI: 10.1371/journal.pone.0024576
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