Skip to main content
U.S. flag

An official website of the United States government

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

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.
Technical Note (NIST TN) - 1472
Report Number


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


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 June 18, 2024)


If you have any questions about this publication or are having problems accessing it, please contact

Created October 12, 2005, Updated January 27, 2020