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RECOMB International Workshop on Comparative Genomics

RECOMB-CG 2017: Comparative Genomics pp 101–115Cite as

New Algorithms for the Genomic Duplication Problem

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 10562))

Abstract

One of evolutionary molecular biology fundamental issues is to discover genomic duplication events and their correspondence to the species tree. Such events can be reconstructed by clustering single gene duplications that are inferred by reconciling a set of gene trees with a species tree. Here we propose the first solution to the genomic duplication problem in which every reconciliation with the minimal number of single gene duplications is allowed and the method of clustering called minimum episodes under the assumption that input gene trees are unrooted. We also present an evaluation study of proposed algorithms on empirical datasets.

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Notes

  1. 1.

    In this article, the notion of the plateau is used exclusively with the duplication cost. In literature, it is often called D-plateau in order to distinguish between plateaus for other costs, e.g. DL-plateau [47].

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Acknowledgements

We would like to thank the reviewers for their detailed comments that allowed us to improve our paper. The support was provided by NCN grants #2015/19/N/ST6/01193 and #2015/19/B/ST6/00726.

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Authors and Affiliations

  1. Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland

    Jarosław Paszek & Paweł Górecki

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  1. Jarosław Paszek
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  2. Paweł Górecki
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Correspondence to Jarosław Paszek .

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Editors and Affiliations

  1. University of Campinas, Campinas, São Paulo, Brazil

    Joao Meidanis

  2. Rice University, Houston, Texas, USA

    Luay Nakhleh

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Paszek, J., Górecki, P. (2017). New Algorithms for the Genomic Duplication Problem. In: Meidanis, J., Nakhleh, L. (eds) Comparative Genomics. RECOMB-CG 2017. Lecture Notes in Computer Science(), vol 10562. Springer, Cham. https://doi.org/10.1007/978-3-319-67979-2_6

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  • DOI: https://doi.org/10.1007/978-3-319-67979-2_6

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