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Bioinformatics Advance Access originally published online on September 16, 2004
Bioinformatics 2005 21(1):20-30; doi:10.1093/bioinformatics/bth468
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Bioinformatics vol. 21 issue 1 © Oxford University Press 2005; all rights reserved.

A memory-efficient algorithm for multiple sequence alignment with constraints

Chin Lung Lu * and Yen Pin Huang

Department of Biological Science and Technology, National Chiao Tung University Hsinchu 300, Taiwan, Republic of China

*To whom correspondence should be addressed.

Motivation: Recently, the concept of the constrained sequence alignment was proposed to incorporate the knowledge of biologists about structures/functionalities/consensuses of their datasets into sequence alignment such that the user-specified residues/nucleotides are aligned together in the computed alignment. The currently developed programs use the so-called progressive approach to efficiently obtain a constrained alignment of several sequences. However, the kernels of these programs, the dynamic programming algorithms for computing an optimal constrained alignment between two sequences, run in O({gamma}n 2) memory, where {gamma} is the number of the constraints and n is the maximum of the lengths of sequences. As a result, such a high memory requirement limits the overall programs to align short sequences~only.

Results: We adopt the divide-and-conquer approach to design a memory-efficient algorithm for computing an optimal constrained alignment between two sequences, which greatly reduces the memory requirement of the dynamic programming approaches at the expense of a small constant factor in CPU time. This new algorithm consumes only O({alpha}n) space, where {alpha} is the sum of the lengths of constraints and usually {alpha} << n in practical applications. Based on this algorithm, we have developed a memory-efficient tool for multiple sequence alignment with constraints.

Availability: http://genome.life.nctu.edu.tw/MUSICME

Contact: cllu{at}mail.nctu.edu.tw

Received on April 20, 2004; revised on July 16, 2004; accepted on August 3, 2004

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Home page
 Nucleic Acids ResHome page
Y.-S. Chung, W.-H. Lee, C. Y. Tang, and C. L. Lu
RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W639 - W644.
[Abstract] [Full Text] [PDF]


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