Handling Permutation in Sequence Comparison: Genome-Wide Enhancer Prediction in Vertebrates by a Novel Non-Linear Alignment Scoring Principle

Dirk Dolle; Juan L. Mateo; Michael P. Eichenlaub; Rebecca Sinn; Robert Reinhardt; Burkhard Höckendorf; Daigo Inoue; Lazaro Centanin; Laurence Ettwiller; Joachim Wittbrodt

doi:10.1371/journal.pone.0141487

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Open Access

Peer-reviewed

Research Article

Handling Permutation in Sequence Comparison: Genome-Wide Enhancer Prediction in Vertebrates by a Novel Non-Linear Alignment Scoring Principle

Dirk Dolle ,

* E-mail: ddd1@sanger.ac.uk (DD); Juan.Mateo@cos.uni-heidelberg.de (JLM); Jochen.Wittbrodt@cos.uni-heidelberg.de (JW)

Current address: Wellcome Trust Sanger Institute, Hinxton, United Kingdom

Affiliations Centre for Organismal Studies (COS) Heidelberg, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany, Hartmut Hoffmann-Berling International Graduate School HBIGS, University of Heidelberg, Heidelberg, Germany
⨯
Juan L. Mateo ,

* E-mail: ddd1@sanger.ac.uk (DD); Juan.Mateo@cos.uni-heidelberg.de (JLM); Jochen.Wittbrodt@cos.uni-heidelberg.de (JW)

Affiliation Centre for Organismal Studies (COS) Heidelberg, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
⨯
Michael P. Eichenlaub,

Affiliations Centre for Organismal Studies (COS) Heidelberg, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany, Hartmut Hoffmann-Berling International Graduate School HBIGS, University of Heidelberg, Heidelberg, Germany
⨯
Rebecca Sinn,

Affiliations Centre for Organismal Studies (COS) Heidelberg, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany, Hartmut Hoffmann-Berling International Graduate School HBIGS, University of Heidelberg, Heidelberg, Germany
⨯
Robert Reinhardt,

Affiliations Centre for Organismal Studies (COS) Heidelberg, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany, Hartmut Hoffmann-Berling International Graduate School HBIGS, University of Heidelberg, Heidelberg, Germany
⨯
Burkhard Höckendorf,

Affiliations Centre for Organismal Studies (COS) Heidelberg, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany, Hartmut Hoffmann-Berling International Graduate School HBIGS, University of Heidelberg, Heidelberg, Germany
⨯
Daigo Inoue,

Affiliation Centre for Organismal Studies (COS) Heidelberg, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
⨯
Lazaro Centanin,

Affiliation Centre for Organismal Studies (COS) Heidelberg, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
⨯
Laurence Ettwiller,

Current address: New England Biolabs Inc. Ipswich, Massachusetts, United States of America

Affiliation Centre for Organismal Studies (COS) Heidelberg, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
⨯
Joachim Wittbrodt

* E-mail: ddd1@sanger.ac.uk (DD); Juan.Mateo@cos.uni-heidelberg.de (JLM); Jochen.Wittbrodt@cos.uni-heidelberg.de (JW)

Affiliation Centre for Organismal Studies (COS) Heidelberg, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
⨯

Handling Permutation in Sequence Comparison: Genome-Wide Enhancer Prediction in Vertebrates by a Novel Non-Linear Alignment Scoring Principle

Dirk Dolle,
Juan L. Mateo,
Michael P. Eichenlaub,
Rebecca Sinn,
Robert Reinhardt,
Burkhard Höckendorf,
Daigo Inoue,
Lazaro Centanin,
Laurence Ettwiller,
Joachim Wittbrodt

Published: October 27, 2015
https://doi.org/10.1371/journal.pone.0141487

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Sequence motif analysis
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Sequence alignment
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Eels
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Enhancer elements
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Genomics
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Multiple alignment calculation
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Gene regulation
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Permutation
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