title: Normalization of affine gap costs used in optimal sequence alignment.
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.
authors.affiliation: Department of Computer Science, Monash University, Australia.
authors.forename: L
authors.initials: L
authors.lastname: Allison
mesh_terms: 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