Normalization of Affine Gap Costs Used in Optimal Sequence Alignment

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Journal of Theoretical Biology 161(2) pp263-269 March 1993

L. Allison

School of Computer Science and Software Engineering, Monash University, Australia 3168

Abstract

It is shown how to normalize the costs of an alignment algorithm that employs affine or linear gap costs. The normalized costs are interpreted as the -log probabilities of the instructions of a finite-state edit-machine. This gives an explicit model relating sequences that can be linked to processes of mutation and evolution.

Paper here: [doi:10.1006/jtbi.1993.1054][4/'03], [sciencedirect][4/'03], [.ps].

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