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

Evidence-ranked motif identification.

Author information

1
Program for Computational Biology and Bioinformatics, Duke University, 102 North Building, Durham, NC 27708, USA.

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.

PMID:
20156354
PMCID:
PMC2872879
DOI:
10.1186/gb-2010-11-2-r19
[Indexed for MEDLINE]
Free PMC Article

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