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.

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 6, 2024)

Issues

If you have any questions about this publication or are having problems accessing it, please contact reflib@nist.gov.

Created October 12, 2005, Updated January 27, 2020