Simulated annealing with injecting star-alignment for multiple sequence alignments

Authors:
Hongwei Huo;Hua Ming
Affiliations:
School of Computer Science and Technology, Xidian University, Xi’an, China;School of Computer Science and Technology, Xidian University, Xi’an, China
Venue:
CIS'05 Proceedings of the 2005 international conference on Computational Intelligence and Security - Volume Part I
Year:
2005

Citing 2
Cited 0

The multiple sequence alignment problem in biology

SIAM Journal on Applied Mathematics
Algorithms on strings, trees, and sequences: computer science and computational biology

Algorithms on strings, trees, and sequences: computer science and computational biology

Quantified Score

Hi-index	0.00

Visualization

Abstract

We present a novel algorithm SASAlignSimulated annealing with star-alignment. In the SASAlign, instead of starting with an initial solution chosen at random, we use the results formed by star-alignment to give a good starting point as the initial solution to the SA for further refinement. The time required by the algorithm scales linearly with the number of sequences in S, linearly with the number of iterations, and cube with the length of the sequences, that is O(Nnl3). Experiments on the BAliBASE benchmark database also show that the proposed algorithm is efficient, and prove to be competitive with and better than the other method HMMT.