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Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
Published on: May 31, 2011
MEME SUITE: tools for motif discovery and searching
Timothy L Bailey1, Mikael Boden, Fabian A Buske
1Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia. t.bailey@imb.uq.edu.au
Nucleic Acids Research
|May 22, 2009
Summary
The MEME Suite web server offers tools for discovering and analyzing sequence motifs, including DNA binding sites and protein domains. It now features the GLAM2 algorithm for motifs with gaps and integrates with Gene Ontology terms for functional analysis.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Sequence motifs are crucial for understanding biological functions like DNA binding and protein interactions.
- Existing tools for motif discovery and analysis have limitations in handling complex patterns and integration.
Purpose of the Study:
- To present the updated MEME Suite web server as a unified platform for motif discovery and analysis.
- To introduce new algorithms and features for enhanced motif identification and functional annotation.
Main Methods:
- The MEME motif discovery algorithm and the new GLAM2 algorithm for gapped motifs.
- Sequence scanning tools (MAST, FIMO, GLAM2SCAN) and motif comparison tools (TOMTOM).
- Integration with Gene Ontology (GO) terms via GOMO for functional analysis and web services via Opal.
Main Results:
- The MEME Suite now supports discovery of motifs with gaps using GLAM2.
- Enhanced output includes sequence LOGOS and direct submission to downstream analysis tools.
- All motif-based tools are accessible as web services, facilitating integration and further research.
Conclusions:
- The updated MEME Suite provides a comprehensive and user-friendly platform for motif discovery, analysis, and functional annotation.
- The integration of new algorithms and web services enhances the utility of the MEME Suite for biological research.
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