Trawler: De novo regulatory motif discovery pipeline for chromatin immunoprecipitation

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

Research output: Contribution to journalArticleResearchpeer-review

61 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 languageEnglish
Pages (from-to)563-565
Number of pages3
JournalNature Methods
Volume4
Issue number7
DOIs
Publication statusPublished - Jul 2007
Externally publishedYes

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