Abstract
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.
Supported by the ESPRIT Long Term Research Programme of the EU under project number 20244 (ALCOM-IT).
Basic Research in Computer Science, Centre of the Danish National Research Foundation.
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© 1998 Springer-Verlag Berlin Heidelberg
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Pedersen, C.N.S., Lyngsø, R., Hein, J. (1998). Comparison of coding DNA. In: Farach-Colton, M. (eds) Combinatorial Pattern Matching. CPM 1998. Lecture Notes in Computer Science, vol 1448. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0030788
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DOI: https://doi.org/10.1007/BFb0030788
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