Trawler: De novo regulatory motif discovery pipeline for chromatin immunoprecipitation

Laurence Ettwiller; Benedict Paten; Mirana Ramialison; Ewan Birney; Joachim Wittbrodt

doi:10.1038/nmeth1061

Trawler: De novo regulatory motif discovery pipeline for chromatin immunoprecipitation

Laurence Ettwiller, Benedict Paten, Mirana Ramialison, Ewan Birney, Joachim Wittbrodt

Research output: Contribution to journal › Article › Research › peer-review

69 Citations (Scopus)

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.

Original language	English
Pages (from-to)	563-565
Number of pages	3
Journal	Nature Methods
Volume	4
Issue number	7
DOIs	https://doi.org/10.1038/nmeth1061
Publication status	Published - Jul 2007
Externally published	Yes

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10.1038/nmeth1061

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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.",

author = "Laurence Ettwiller and Benedict Paten and Mirana Ramialison and Ewan Birney and Joachim Wittbrodt",

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AU - Wittbrodt, Joachim

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Trawler: De novo regulatory motif discovery pipeline for chromatin immunoprecipitation

Abstract

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