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Composition Alignment

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Algorithms in Bioinformatics (WABI 2003)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 2812))

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Abstract

In this paper, we develop a new approach for analyzing DNA sequences in order to detect regions with similar nucleotide composition. Our algorithm, which we call composition alignment or, more whimsically, scrambled alignment, employs the mechanisms of string matching and string comparison yet avoids the overdependence of those methods on position-by-position matching. In composition alignment, we extend the matching concept to composition matching. Two strings have a composition match if their lengths are equal and they have the same nucleotide content.

We define the composition alignment problem and give a dynamic programming solution. We explore several composition match weighting functions and show that composition alignment with one class of these can be computed in O(nm) time, the same as for standard alignment. We discuss statistical properties of composition alignment scores and demonstrate the ability of the algorithm to detect regions of similar composition in eukaryotic promoter sequences in the absence of detectable similarity through standard alignment.

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Author information

Authors and Affiliations

  1. Department of Biomathematical Sciences, The Mount Sinai School of Medicine, New York, NY, 10029-6574, USA

    Gary Benson

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  1. Gary Benson
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Editors and Affiliations

  1. Department of Biomathematical Sciences, The Mount Sinai School of Medicine, 10029-6574, New York, NY

    Gary Benson

  2. Institute of Biomedical and Life Sciences, Division of Environmental and Evolutionary Biology, University of Glasgow, G12 8QQ, Glasgow, Scotland

    Roderic D. M. Page

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© 2003 Springer-Verlag Berlin Heidelberg

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Benson, G. (2003). Composition Alignment. In: Benson, G., Page, R.D.M. (eds) Algorithms in Bioinformatics. WABI 2003. Lecture Notes in Computer Science(), vol 2812. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-39763-2_32

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  • DOI: https://doi.org/10.1007/978-3-540-39763-2_32

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-20076-5

  • Online ISBN: 978-3-540-39763-2

  • eBook Packages: Springer Book Archive

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