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
Conference Dates: November 20-21, 2003
Conference Location: Pittsburgh, PA
Conference Title: Biological Language Conference
Pub Type: Conferences
linear programming, Markov decision process, multiple sequence alignment