^Bioinformatics^ ^#Alignment^

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

Normalization of Affine Gap Costs Used in Optimal Sequence Alignment

L. Allison

School of Computer Science and Software Engineering, Monash University, Australia 3168,
http://www.csse.monash.edu.au/~lloyd/tildeStrings

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. Copyright 1993, 1999 Academic Press

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

Was: [idealibrary]['02], [pdf]['02]



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