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Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation

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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Figure 1: The Trawler pipeline.
Figure 2: Performances of Trawler.

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Acknowledgements

We thank A. Budd and T. Henrich for critical reading of the manuscript, and the Wittbrodt laboratory members for stimulating input to the project. This work was supported by a European Union framework program 6 grant (STREP Hygia) to J.W.

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Authors and Affiliations

Authors

Contributions

L.E. and B.P. developed the algorithm with contribution from M.R.; L.E. and M.R. tested the algorithm; M.R. and L.E. implemented the website; L.E., M.R. and J.W. wrote the manuscript with contribution from B.P. and E.B.

Corresponding author

Correspondence to Joachim Wittbrodt.

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Competing interests

The authors declare no competing financial interests.

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Supplementary Figures 1–5, Supplementary Tables 1–2, Supplementary Note, Supplementary Methods (PDF 3080 kb)

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Ettwiller, L., Paten, B., Ramialison, M. et al. Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation. Nat Methods 4, 563–565 (2007). https://doi.org/10.1038/nmeth1061

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