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Evidence-ranked motif identification.

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.

SUBMITTER: Georgiev S

PROVIDER: S-EPMC2872879 | biostudies-other | 2010

REPOSITORIES: biostudies-other

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Evidence-ranked motif identification.

Georgiev Stoyan S Boyle Alan P AP Jayasurya Karthik K Ding Xuan X Mukherjee Sayan S Ohler Uwe U

Genome biology 20100215 2

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 o ...[more]

PMID: 20156354

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