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Models and Algorithms for Genome Evolution pp 183–206Cite as

A Retrospective on Genomic Preprocessing for Comparative Genomics

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Part of the book series: Computational Biology ((COBO,volume 19))

Abstract

In this paper, we present a survey of research on genomic preprocessing for comparative genomics, i.e., handling genomes with gene repetitions, missing or redundant genes, initiated by David Sankoff in 1999. The development of this research ends with several interesting results within and beyond computational biology and bioinformatics, with possible new contributions in the future. We will describe the history of development of this research and review the current status of the corresponding problems. For the problem of handling missing genes (scaffold filling), we also present some technical details which are not given in the previous papers. Some open problems will be listed at the end for further research.

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Acknowledgements

I would like to thank my collaborators for this series of research: Zhixiang Chen, Richard Fowler, Bin Fu, Haitao Jiang, Minghui Jiang, Zhong Li, Guohui Lin, Nan Liu, David Sankoff, Weitian Tong, Lusheng Wang, Boting Yang, Zhiyu Zhao, Chunfang Zheng and Daming Zhu.

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  1. Department of Computer Science, Montana State University, Bozeman, MT, 59717-3880, USA

    Binhai Zhu

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  1. Binhai Zhu
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Correspondence to Binhai Zhu .

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Editors and Affiliations

  1. Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada

    Cedric Chauve

  2. Computer Science and Operations Research, University of Montreal, Montreal, Québec, Canada

    Nadia El-Mabrouk

  3. Biometry and Evolutionary Biology, INRIA Rhône-Alpes, University of Lyon, Villeurbanne, France

    Eric Tannier

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Zhu, B. (2013). A Retrospective on Genomic Preprocessing for Comparative Genomics. In: Chauve, C., El-Mabrouk, N., Tannier, E. (eds) Models and Algorithms for Genome Evolution. Computational Biology, vol 19. Springer, London. https://doi.org/10.1007/978-1-4471-5298-9_9

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  • DOI: https://doi.org/10.1007/978-1-4471-5298-9_9

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