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International Computing and Combinatorics Conference

COCOON 2001: Computing and Combinatorics pp 86–90Cite as

A Greedy Algorithm for Optimal Recombination

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Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2108))

Abstract

Let Σ be an alphabet and Σn denote the collection of all sequences of length n over Σ. For any s1 = a1a2...ajaj+1...an, s2= b1b2...bj bj+1...bn € Sn, a recombination of s1 and s2 at position j is de?ned as an operation that crosses s1 and s2 at position j and generates t1=a1a2...ajbj+1...bn and t2=b1b2...bjaj+1... an. Denote A and S two collections of sequences. In this paper, we discuss generating A from S by a series of recombinations in minimum number of steps. We present a greedy algorithm for ?nding the optimal recombination evolutionary history from S to any tree A of sequences when |S|=2.

Research supported in part by NIH Grant RO1 GM62118 (to X.G.) and NSF of China (19771025). Wu is on leave from Math Dept,N.U.D.T.,Hunan 410073,China.

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References

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  5. Kececioglu, J. and Gusfield, D., 1994. Reconstructing a history of recombinations from a set of sequences, 5th Annual ACM-SIAM Symposium on Discrete Algorithm Arlington, Virginia, pp.471–480. Also in Discrete Applied Mathematics 88(1998)239-260.

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Author information

Authors and Affiliations

  1. Center of Bioinformatics and Biological Statistics, Iowa State University, Ames, IA, 50011, USA

    Shiquan Wu & Xun Gu

Authors
  1. Shiquan Wu
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  2. Xun Gu
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Editor information

Editors and Affiliations

  1. Department of Computer Science, University of Massachusetts, One University Avenue, Lowell, MA, 01854, USA

    Jie Wang

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© 2001 Springer-Verlag Berlin Heidelberg

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Cite this paper

Wu, S., Gu, X. (2001). A Greedy Algorithm for Optimal Recombination. In: Wang, J. (eds) Computing and Combinatorics. COCOON 2001. Lecture Notes in Computer Science, vol 2108. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-44679-6_10

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  • DOI: https://doi.org/10.1007/3-540-44679-6_10

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-42494-9

  • Online ISBN: 978-3-540-44679-8

  • eBook Packages: Springer Book Archive

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