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Normalisation of Affine Gap Costs used in Optimal Sequence Alignment. Lloyd Allison,

Summary: Normalisation of Affine Gap Costs used in Optimal Sequence Alignment.
Lloyd Allison,
Department of Computer Science,
Monash University,
Australia 3168.
email: lloyd@cs.monash.edu.au
Partially supported by an Australian Research Council grant.
Feb 1992
revised Sep 1992
Abstract. It is shown how to normalise the costs of an alignment algorithm that employs affine or linear
gap costs. The normalised costs are interpreted as the ­log probabilities of the instructions of a finite­state
edit­machine. This gives an explicit model relating sequences that can be linked to processes of mutation
and evolution.
Keywords: affine, alignment, edit distance, gap, indel, linear, model, normalisation.
1. Introduction.
Alignment algorithms are in common use in Molecular Biology and in other disciplines[$Need,
$Sank, $Myer] to calculate an edit­distance between a pair of sequences, such as two DNA or protein
sequences. A cost is assigned to an alignment by a cost function, often having one or more parameters or
weights. An alignment algorithm finds an optimal alignment having minimum cost under its cost function.
(Equivalently a similarity score can be assigned and the algorithm finds an alignment having a maximum


Source: Allison, Lloyd - Caulfield School of Information Technology, Monash University


Collections: Computer Technologies and Information Sciences