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Nat Protoc. 2014;9(6):1428-50. doi: 10.1038/nprot.2014.083. Epub 2014 May 22.

Motif-based analysis of large nucleotide data sets using MEME-ChIP.

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Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
1] Department of Genome Sciences, University of Washington, Seattle, Washington, USA. [2] Department of Computer Science and Engineering, University of Washington, Seattle, Washington, USA.
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.


MEME-ChIP is a web-based tool for analyzing motifs in large DNA or RNA data sets. It can analyze peak regions identified by ChIP-seq, cross-linking sites identified by CLIP-seq and related assays, as well as sets of genomic regions selected using other criteria. MEME-ChIP performs de novo motif discovery, motif enrichment analysis, motif location analysis and motif clustering, providing a comprehensive picture of the DNA or RNA motifs that are enriched in the input sequences. MEME-ChIP performs two complementary types of de novo motif discovery: weight matrix-based discovery for high accuracy; and word-based discovery for high sensitivity. Motif enrichment analysis using DNA or RNA motifs from human, mouse, worm, fly and other model organisms provides even greater sensitivity. MEME-ChIP's interactive HTML output groups and aligns significant motifs to ease interpretation. This protocol takes less than 3 h, and it provides motif discovery approaches that are distinct and complementary to other online methods.

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