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Bioinformatics Vol. 18 no. 90002 2002
Pages S116-S127
© 2002 Oxford University Press

Contextual alignment of biological sequences (Extended abstract)

Anna Gambin 1, Slawomir Lasota 1, Radoslaw Szklarczyk 1, Jerzy Tiuryn 1 and Jerzy Tyszkiewicz 1

1 Institute of Informatics, Warsaw University, Banacha 2, 02-097, Warsaw, Poland

Received on April 8, 2002 ; accepted on June 15, 2002

We present a model of contextual alignment of biological sequences. It is an extension of the classical alignment, in which we assume that the cost of a substitution depends on the surrounding symbols. In this model the cost of transforming one sequence into another depends on the order of editing operations. We present efficient algorithms for calculating this cost, as well as reconstructing (the representation of) all the orders of operations which yield this optimal cost. A precise characterization of the families of linear orders which can emerge this way is given.

Contact: jty{at}mimuw.edu.pl


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