Sensitivity of Multiple Sequence Alignments to Perturbations in Cost Matrices
Fern Y. Hunt, Agnes A. O'Gallagher
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.
Karush-Kuhn-Tucker theorem, linear programming, multiple sequence alignment, sensitivity
and O'Gallagher, A.
Sensitivity of Multiple Sequence Alignments to Perturbations in Cost Matrices, Technical Note (NIST TN), National Institute of Standards and Technology, Gaithersburg, MD
(Accessed February 27, 2024)