Efficient Constrained Multiple Sequence Alignment with Performance Guarantee

Authors:
Francis Y. L. Chin;N. L. Ho;T. W. Lam;Prudence W. H. Wong;M. Y. Chan
Affiliations:
-;-;-;-;-
Venue:
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Year:
2003

Citing 6
Cited 6

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Abstract

The Constrained Multiple Sequence Alignment problemis to align a set of sequences subject to a given constrainedsequence, which arises from some knowledge of the structureof the sequences. This paper presents new algorithmsfor this problem, which are more efficient in terms of timeand space (memory) than the previous algorithms [14], andwith a worst-case guarantee on the quality of the alignment.Saving the space requirement by a quadratic factor is particularlysignificant as the previous O(n4)-space algorithmhas limited application due to its huge memory requirement.Experiments on real data sets confirm that our new algorithmsshow improvements in both alignment quality andresource requirements.