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

Wenxiu Ma1, William S Noble2, Timothy L Bailey3

  • 1Department of Genome Sciences, University of Washington, Seattle, Washington, USA.

Nature Protocols
|May 24, 2014
PubMed
Summary
This summary is machine-generated.

MEME-ChIP is a web tool for DNA and RNA motif discovery. It offers de novo motif discovery, enrichment, location, and clustering for ChIP-seq and CLIP-seq data.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Analyzing DNA and RNA motifs is crucial for understanding gene regulation.
  • Existing tools may lack comprehensive analysis or specific functionalities for large datasets.

Purpose of the Study:

  • To introduce MEME-ChIP, a web-based tool for comprehensive motif analysis in large DNA and RNA datasets.
  • To provide complementary de novo motif discovery approaches for enhanced sensitivity and accuracy.

Main Methods:

  • MEME-ChIP analyzes peak regions from ChIP-seq and cross-linking sites from CLIP-seq.
  • It performs de novo motif discovery using weight matrix (accuracy) and word-based (sensitivity) methods.
  • Enrichment analysis utilizes motif databases from various model organisms.

Main Results:

  • MEME-ChIP offers de novo motif discovery, enrichment, location analysis, and clustering.
  • The tool provides a comprehensive view of enriched DNA and RNA motifs.
  • Interactive HTML output facilitates motif interpretation through grouping and alignment.

Conclusions:

  • MEME-ChIP is an efficient (under 3 hours) and comprehensive tool for motif analysis.
  • It offers distinct and complementary approaches to existing online methods.
  • The tool aids in understanding biological sequence patterns from various high-throughput assays.