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IEEE Computer Society Bioinformatics Conference (CSB'02)   p. 127
Constrained Multiple Sequence Alignment Tool Development and Its Application to RNase Family Alignment
Chuan Yi Tang, National Tsing Hua University
Chin Lung Lu, National Center for High-Performance Computing
Margaret Dah-Tsyr Chang, National Tsing Hua University
Yin-Te Tsai, Providence University
Yuh-Ju Sun, National Tsing Hua University
Kun-Mao Chao, National Yang-Ming University
Jia-Ming Chang, National Tsing Hua University
Yu-Han Chiou, National Tsing Hua University
Chia-Mao Wu, National Tsing Hua University
Hao-Teng Chang, National Tsing Hua University
Wei-I Chou, National Tsing Hua University

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DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/CSB.2002.1039336
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Abstract
In this paper, we design an algorithm of computing a constraine multiple sequence alignment (CMSA for short) for guaranteeing that the generated alignment satisfies the user-specified constraints that some particular residues should be aligned together. If the number of residues needed to be aligned together is a constant α, then the time-complexity of our CMSA algorithm for aligning K sequences is O (αKn4), where n is the maximum of the lengths of sequences. In addition, we have build up such a CMSA software system and made several experiments on the RNase sequences, which mainly function in catalyzing the degradation of RNA molecules. The resulting alignments illustrate the practicability of our method.
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Citation:  Chuan Yi Tang, Chin Lung Lu, Margaret Dah-Tsyr Chang, Yin-Te Tsai, Yuh-Ju Sun, Kun-Mao Chao, Jia-Ming Chang, Yu-Han Chiou, Chia-Mao Wu, Hao-Teng Chang, Wei-I Chou, "Constrained Multiple Sequence Alignment Tool Development and Its Application to RNase Family Alignment," csb, p. 127,  IEEE Computer Society Bioinformatics Conference (CSB'02),  2002