Evidence-ranked motif identification

Genome Biol. 2010;11(2):R19. doi: 10.1186/gb-2010-11-2-r19. Epub 2010 Feb 15.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Computational Biology
  • DNA, Fungal / genetics
  • Genome, Human
  • Genome-Wide Association Study / methods*
  • Humans
  • Mice
  • Oligonucleotide Array Sequence Analysis*
  • Sequence Analysis, DNA / methods*


  • DNA, Fungal