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International Workshop on Algorithms in Bioinformatics

WABI 2002: Algorithms in Bioinformatics pp 126–139Cite as

Segment Match Refinement and Applications

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Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2452))

Abstract

Comparison of large, unfinished genomic sequences requires fast methods that are robust to misordering, misorientation, and duplications. A number of fast methods exist that can compute local similarities between such sequences, from which an optimal one-to-one correspondence might be desired. However, existing methods for computing such a correspondence are either too costly to run or are inappropriate for unfinished sequence. We propose an efficient method for refining a set of segment matches such that the resulting segments are of maximal size without non-identity overlaps. This resolved set of segments can be used in various ways to compute a similarity measure between any two large sequences, and hence can be used in alignment, matching, or tree construction algorithms for two or more sequences.

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Author information

Authors and Affiliations

  1. Informatics Research, Celera Genomics Corp., 45 W Gude Drive, 20850, Rockville, MD, USA

    Aaron L. Halpern, Daniel H. Huson & Knut Reinert

Authors
  1. Aaron L. Halpern
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  2. Daniel H. Huson
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  3. Knut Reinert
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Editor information

Editors and Affiliations

  1. IMIM-UPF-CRG, Dr. Aiguader 80, 08003, Barcelona, Spain

    Roderic Guigó

  2. Department of Computer Science, University of California, 95616, Davis, CA, USA

    Dan Gusfield

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© 2002 Springer-Verlag Berlin Heidelberg

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Halpern, A.L., Huson, D.H., Reinert, K. (2002). Segment Match Refinement and Applications. In: Guigó, R., Gusfield, D. (eds) Algorithms in Bioinformatics. WABI 2002. Lecture Notes in Computer Science, vol 2452. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45784-4_10

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  • DOI: https://doi.org/10.1007/3-540-45784-4_10

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-44211-0

  • Online ISBN: 978-3-540-45784-8

  • eBook Packages: Springer Book Archive

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