Comparison of Coding DNA

  • Christian N. S. Pedersen
  • Rune B. Lyngsø
  • Jotun Hein


We discuss a model for the evolutionary distance between two coding DNA sequences which specializes to the DNA/protein model proposed in Hein [3]. 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 [3] and we believe that the constant factor of the running time is sufficiently small to make the algorithm feasible in practice.
How to Cite
Pedersen, C., Lyngsø, R., & Hein, J. (1998). Comparison of Coding DNA. BRICS Report Series, 5(3).