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Multiple Genome Alignment: Chaining Algorithms Revisited

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Combinatorial Pattern Matching (CPM 2003)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2676))

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Abstract

Given n fragments from k > 2 genomes, we will show how to find an optimal chain of colinear non-overlapping fragments in time O(n logk−2 n log log n) and space O(n logk−2 n). Our result solves an open problem posed by Myers and Miller because it reduces the time complexity of their algorithm by a factor log2 n / log log n and the space complexity by a factor log n. For k = 2 genomes, our algorithm takes O(n log n) time and O(n) space.

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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, Albert-Einstein-Allee, 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. Depto. de Ciencias de la Computación, Universidad de Chile, Blanco Encalada 2120, Santiago, 6511224, Chile

    Ricardo Baeza-Yates

  2. Escuela de Ciencias Físico-Matemáticas, Universidad Michoacana, Edificio “B”, ciudad universitaria, Morelia Michoacán, Mexico

    Edgar Chávez

  3. Université de Marne-la-Vallée, 77454, Marne-la-Vallée Cedex 2, France

    Maxime Crochemore

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© 2003 Springer-Verlag Berlin Heidelberg

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Abouelhoda, M.I., Ohlebusch, E. (2003). Multiple Genome Alignment: Chaining Algorithms Revisited. In: Baeza-Yates, R., Chávez, E., Crochemore, M. (eds) Combinatorial Pattern Matching. CPM 2003. Lecture Notes in Computer Science, vol 2676. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-44888-8_1

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  • DOI: https://doi.org/10.1007/3-540-44888-8_1

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-40311-1

  • Online ISBN: 978-3-540-44888-4

  • eBook Packages: Springer Book Archive

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