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PUBLICATIONS

Sensitivity of Multiple Sequence Alignments to Perturbations in Cost Matrices

Published

Author(s)

Fern Y. Hunt, Agnes A. O'Gallagher

Abstract

A description of a new method for aligning biological sequences is presented. It is based on a formulation as a Markov decision optimization problem. Alignment is obtained by solving an associated linear programming problem. In this paper we show that the sensitivity of the alignment to changes in the cost matrices can be quanitified. This is in contrast to conventional dynamic programming based methods.
Citation
Technical Note (NIST TN) - 1472
Report Number
1472
NIST Pub Series
Technical Note (NIST TN)
Pub Type
NIST Pubs

Keywords

Karush-Kuhn-Tucker theorem, linear programming, multiple sequence alignment, sensitivity

Citation

Hunt, F. and O'Gallagher, A. (2005), Sensitivity of Multiple Sequence Alignments to Perturbations in Cost Matrices, Technical Note (NIST TN), National Institute of Standards and Technology, Gaithersburg, MD (Accessed October 8, 2025)

Issues

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Created October 12, 2005, Updated January 27, 2020
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