Normalization of Affine Gap Costs Used in Optimal Sequence Alignment
L. Allison, Journal of Theoretical Biology, 161(2), pp.263-269, doi:10.1006/jtbi.1993.1054, March 1993
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], [preprint.ps].