Efficient constrained multiple sequence alignment with performance guarantee

The constrained multiple sequence alignment problem is to align a set of sequences subject to a given constrained sequence, which arises from some knowledge of the structure of the sequences. This paper presents new algorithms for this problem, which are more efficient in terms of time and space (me...

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Bibliographic Details
Published in2nd IEEE Computer Society Bioinformatics Conference (CSB 2003) Vol. 2; pp. 337 - 346
Main Authors Francis YL Chin, Ho, N.L., Lam, T.W., Prudence WH Wong, Chan, M.Y.
Format Conference Proceeding Journal Article
LanguageEnglish
Published United States IEEE 2003
Subjects
Algorithms
Amino Acid Sequence
Base Sequence
Biological control systems
Biology computing
Computational biology
Computer science
Costs
Degradation
Heuristic algorithms
Information systems
Molecular Sequence Data
Pattern Recognition, Automated - methods
RNA
Sequence Alignment - methods
Sequence Analysis - methods
Sequences
Software
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ISBN0769520006
9780769520001
ISSN1555-3930
DOI10.1109/CSB.2003.1227334

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Summary:The constrained multiple sequence alignment problem is to align a set of sequences subject to a given constrained sequence, which arises from some knowledge of the structure of the sequences. This paper presents new algorithms for this problem, which are more efficient in terms of time and space (memory) than the previous algorithms and with a worst-case guarantee on the quality of the alignment. Saving the space requirement by a quadratic factor is particularly significant as the previous O(n/sup 4/)-space algorithm has limited application due to its huge memory requirement. Experiments on real data sets confirm that our new algorithms show improvements in both alignment quality and resource requirements.
ISBN:0769520006
9780769520001
ISSN:1555-3930
DOI:10.1109/CSB.2003.1227334