Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation (original) (raw)

Nature Methods volume 4, pages 563–565 (2007)Cite this article

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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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

  1. Developmental Biology Unit, EMBL-Heidelberg, Meyerhofstraße 1, Heidelberg, 69017, Germany
    Laurence Ettwiller, Mirana Ramialison & Joachim Wittbrodt
  2. European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 ISD, UK
    Benedict Paten & Ewan Birney

Authors

  1. Laurence Ettwiller
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  2. Benedict Paten
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  3. Mirana Ramialison
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  4. Ewan Birney
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  5. Joachim Wittbrodt
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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 toJoachim Wittbrodt.

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The authors declare no competing financial interests.

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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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