Sequence Alignment Algorithms for Run-Length-Encoded Strings

  • Guan Shieng Huang
  • Jia Jie Liu
  • Yue Li Wang
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5092)


A unified framework is applied to solving various sequence comparison problems for run-length encoded strings. All of these algorithms take O( min {mn′,mn}) time and O( max {m,n}) space, for two strings of lengths m and n, with m′ and n′ runs, respectively. We assume the linear-gap model and make no assumption on the scoring matrices, which maximizes the applicability of these algorithms. The trace (i.e., the way to align two strings) of an optimal solution can also be recovered within the same time and space bounds.


Edit Distance Global Alignment Edit Graph Alignment Problem Longe Common Subsequence 
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 2008

Authors and Affiliations

  • Guan Shieng Huang
    • 1
  • Jia Jie Liu
    • 2
  • Yue Li Wang
    • 1
  1. 1.Department of Computer Science and Information EngineeringNational Chi Nan UniversityTaiwan
  2. 2.Department of Information ManagementShih Hsin UniversityTaiwan

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