Constrained multiple sequence alignment tool development and its application to RNase family alignment.

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.

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Peer reviewed

Constrained multiple sequence alignment tool development and its application to RNase family alignment.

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, …

Journal of bioinformatics and computational biology, Vol.1(2), pp.267-287

07/2003

Abstract

In this paper, we design a heuristic algorithm of computing a constrained 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 alpha, then the time-complexity of our CMSA algorithm for aligning K sequences is O(alphaKn(4)), where n is the maximum of the lengths of sequences. In addition, we have built 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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Title: Constrained multiple sequence alignment tool development and its application to RNase family alignment.
Creators - without role: Chuan Yi Tang - Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC.
Chin Lung Lu - Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC.
Margaret Dah-Tsyr Chang - Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC.
Yin-Te Tsai - Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC.
Yuh-Ju Sun - Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC.
Kun-Mao Chao - National Tsing Hua University
Jia-Ming Chang - Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC.
Yu-Han Chiou - Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC.
Chia-Mao Wu - Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC.
Hao-Teng Chang - Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC.
Wei-I Chou - Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC.
Identifiers: 9957773463106774
Academic Unit: Department of Computer Science, College of Electrical Engineering and Computer Science, National Tsing Hua University; Ph.D. Program in Bioindustria; Technology, College of Life Science, National Tsing Hua University
Language: English
Resource Type: Journal article
Publication Details: Journal of bioinformatics and computational biology, Vol.1(2), pp.267-287

Constrained multiple sequence alignment tool development and its application to RNase family alignment.

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