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International Workshop on Algorithms in Bioinformatics

WABI 2003: Algorithms in Bioinformatics pp 1–16Cite as

A Local Chaining Algorithm and Its Applications in Comparative Genomics

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

Abstract

Given fragments from multiple genomes, we will show how to find an optimal local chain of colinear non-overlapping fragments in sub-quadratic time, using methods from computational geometry. A variant of the algorithm finds all significant local chains of colinear non-overlapping fragments. The local chaining algorithm can be used in a variety of problems in comparative genomics: The identification of regions of similarity (candidate regions of conserved synteny), the detection of genome rearrangements such as transpositions and inversions, and exon prediction.

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Author information

Authors and Affiliations

  1. Faculty of Technology, University of Bielefeld, P.O. Box 10 01 31, 33501, Bielefeld, Germany

    Mohamed Ibrahim Abouelhoda

  2. Faculty of Computer Science, University of Ulm, 89069, Ulm, Germany

    Enno Ohlebusch

Authors
  1. Mohamed Ibrahim Abouelhoda
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  2. Enno Ohlebusch
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Editor information

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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Abouelhoda, M.I., Ohlebusch, E. (2003). A Local Chaining Algorithm and Its Applications in Comparative Genomics. 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_1

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  • DOI: https://doi.org/10.1007/978-3-540-39763-2_1

  • 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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