Normalization of affine gap costs used in optimal sequence alignment.
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.
Allison
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Department of Computer Science, Monash University, Australia.
D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D003198:Computer Simulation; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D011336:Probability; D016415:Sequence Alignment