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Evidence-ranked motif identification

Authors

  • S. Georgiev
  • A.P. Boyle
  • K. Jayasurya
  • X. Ding
  • S. Mukherjee
  • U. Ohler

Journal

  • Genome Biology

Citation

  • Genome Biol 11 (2): R19

Abstract

  • cERMIT is a computationally efficient motif discovery tool based on analyzing genome-wide quantitative regulatory evidence. Instead of pre-selecting promising candidate sequences, it utilizes information across all sequence regions to search for high-scoring motifs. We apply cERMIT on a range of direct binding and overexpression datasets; it substantially outperforms state-of-the-art approaches on curated ChIP-chip datasets, and easily scales to current mammalian ChIP-seq experiments with data on thousands of non-coding regions.


DOI

doi:10.1186/gb-2010-11-2-r19