Comparison of coding DNA

  • Christian N. S. Pedersen
  • Rune Lyngsø
  • Jotun Hein
Session IV
Part of the Lecture Notes in Computer Science book series (LNCS, volume 1448)


We discuss a model for the evolutionary distance between two coding DNA sequences which specializes to the DNA/protein model proposed in Hein [4]. We discuss the DNA/protein model in details and present a quadratic time algorithm that computes an optimal alignment of two coding DNA sequences in the model under the assumption of affine gap cost. The algorithm solves a conjecture in [4] and we believe that the constant factor of the running time is sufficiently small to make the algorithm feasible in practice.


Alignment Algorithm Optimal Alignment Table Entry Level Cost Eleven Type 
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Copyright information

© Springer-Verlag Berlin Heidelberg 1998

Authors and Affiliations

  • Christian N. S. Pedersen
    • 1
  • Rune Lyngsø
    • 1
  • Jotun Hein
    • 2
  1. 1.BRICS, Department of Computer ScienceUniversity of AarhusÅrhus CDenmark
  2. 2.Department of Ecology and GeneticsUniversity of AarhusÅrhus CDenmark

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