doi: 10.1038/nmeth1061.
Epub 2007 Jun 24.
Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation
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- PMID: 17589518
- DOI: 10.1038/nmeth1061
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Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation
Nat Methods.
2007 Jul.
Abstract
We developed Trawler, the fastest computational pipeline to date, to efficiently discover over-represented motifs in chromatin immunoprecipitation (ChIP) experiments and to predict their functional instances. When we applied Trawler to data from yeast and mammals, 83% of the known binding sites were accurately called, often with other additional binding sites, providing hints of combinatorial input. Newly discovered motifs and their features (identity, conservation, position in sequence) are displayed on a web interface.
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