Efficient constrained multiple sequence alignment with performance guarantee

• Published in: 2nd 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
• Language: English
• 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
• ISBN: 0769520006; 9780769520001
• ISSN: 1555-3930
• DOI: 10.1109/CSB.2003.1227334

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.