Comparison of Coding DNA

Christian N. S. Pedersen
Rune B. Lyngsų
Jotun Hein

January 1998


We discuss a model for the evolutionary distance between two coding DNA sequences which specializes to the DNA/protein model proposed in by Hein in the paper ``An algorithm combining DNA and protein alignment''. 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. We believe that the constant factor of the running time is sufficiently small to make the algorithm feasible in practice

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