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Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes

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Algorithms in Bioinformatics (WABI 2009)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5724))

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Abstract

The existing synteny block reconstruction algorithms use anchors (e.g., orthologous genes) shared over all genomes to construct the synteny blocks for multiple genomes. This approach, while efficient for a few genomes, cannot be scaled to address the need to construct synteny blocks in many mammalian genomes that are currently being sequenced. The problem is that the number of anchors shared among all genomes quickly decreases with the increase in the number of genomes. Another problem is that many genomes (plant genomes in particular) had extensive duplications, which makes decoding of genomic architecture and rearrangement analysis in plants difficult. The existing synteny block generation algorithms in plants do not address the issue of generating non-overlapping synteny blocks suitable for analyzing rearrangements and evolution history of duplications. We present a new algorithm based on the A-Bruijn graph framework that overcomes these difficulties and provides a unified approach to synteny block reconstruction for multiple genomes, and for genomes with large duplications.

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Author information

Authors and Affiliations

  1. Department of Computer Science and Engineering, USA

    Qian Peng & Pavel A. Pevzner

  2. Department of Mathematics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA

    Glenn Tesler

  3. Department of Computer Science and Engineering, University of South Carolina, 315 Main St., Columbia, SC, 29208, USA

    Max A. Alekseyev

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  1. Qian Peng
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  2. Max A. Alekseyev
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  3. Glenn Tesler
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  4. Pavel A. Pevzner
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Editors and Affiliations

  1. Center for Bioinformatics and Computational Biology, and Department of Computer Science, University of Maryland, MD, College Park, USA

    Steven L. Salzberg

  2. Department of Computer Sciences, The University of Texas at Austin, TX, USA

    Tandy Warnow

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© 2009 Springer-Verlag Berlin Heidelberg

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Peng, Q., Alekseyev, M.A., Tesler, G., Pevzner, P.A. (2009). Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes. In: Salzberg, S.L., Warnow, T. (eds) Algorithms in Bioinformatics. WABI 2009. Lecture Notes in Computer Science(), vol 5724. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04241-6_19

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  • DOI: https://doi.org/10.1007/978-3-642-04241-6_19

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-04240-9

  • Online ISBN: 978-3-642-04241-6

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