Nature Methods
- 4, 563 - 565 (2007)
Published online: 24 June 2007; | doi:10.1038/nmeth1061
Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitationLaurence Ettwiller1, Benedict Paten2, Mirana Ramialison1, Ewan Birney2 & Joachim Wittbrodt11
Developmental Biology Unit, EMBL-Heidelberg, Meyerhofstra e 1, 69017 Heidelberg, Germany. 2
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 ISD Cambridge, UK.
Correspondence should be addressed to Joachim Wittbrodt wittbrodt@embl.de 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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