Constructing Sequence Alignments from a Markov Decision Model with Estimated Parameter Values

Published

January 1, 2004

Author(s)

Fern Y. Hunt, Anthony J. Kearsley, Agnes A. O'Gallagher

Abstract

Current methods for aligning biological sequences are based on dynamic programming algorithms. If large numbers of sequences or a number of long ones are to be aligned the required computations are expensive in memory and CPU time. In an attempt to bring the tools of large scale linear programming (LP) methods to bear on this problem, we formulate the alignment process as a controlled Markov chain and construct a suggested alignment based on policies that minimize the expected total cost of the alignment.

Proceedings Title

2003 Proceedings of the Biological Language Conference, Pittsburgh, PA, Nov. 20-21, 2003
and Applied Bioinformatics

Volume

3

Issue

(2-3)

Conference Dates

November 20-21, 2003

Conference Location

Pittsburgh, PA

Conference Title

Biological Language Conference

Pub Type

Conferences

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Keywords

linear programming, Markov decision process, multiple sequence alignment

Citation

Hunt, F. , Kearsley, A. and O'Gallagher, A. (2004), Constructing Sequence Alignments from a Markov Decision Model with Estimated Parameter Values, 2003 Proceedings of the Biological Language Conference, Pittsburgh, PA, Nov. 20-21, 2003 and Applied Bioinformatics, Pittsburgh, PA, [online], https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=51306 (Accessed October 24, 2025)