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Determining DNA sequence similarity using maximum independent set algorithms for interval graphs

  • Deborah Joseph
  • Joao Meidanis
  • Prasoon Tiwari
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 621)

Abstract

Motivated by the problem of finding similarities in DNA and amino acid sequences, we study a particular class of two dimensional interval graphs and present an algorithm that finds a maximum weight “increasing” independent set for this class. Our class of interval graphs is a subclass of the graphs with interval number 2. The algorithm we present runs in O(n log n) time, where n is the number of nodes, and its implementation provides a practical solution to a common problem in genetic sequence comparison.

Keywords

Maximum Weight Query Sequence Interval Graph Interval Number Response Sequence 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 1992

Authors and Affiliations

  • Deborah Joseph
    • 1
  • Joao Meidanis
    • 1
  • Prasoon Tiwari
    • 1
  1. 1.Computer Sciencés DepartmentUniversity of Wisconsin-MadisonMadisonUSA

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