Constrained Multiple Sequence Alignment Tool Development and Its Application to RNase Family Alignment-Reference-Cited by-同舟云学术

Constrained Multiple Sequence Alignment Tool Development and Its Application to RNase Family Alignment

Published:2003-07 Issue:02 Volume:01 Page:267-287
ISSN:0219-7200
Container-title:Journal of Bioinformatics and Computational Biology
language:en
Short-container-title:J. Bioinform. Comput. Biol.

Author:

Tang Chuan Yi¹,Lu Chin Lung²,Chang Margaret Dah-Tsyr³,Tsai Yin-Te⁴,Sun Yuh-Ju³,Chao Kun-Mao⁵,Chang Jia-Ming¹,Chiou Yu-Han¹,Wu Chia-Mao³,Chang Hao-Teng³,Chou Wei-I³

Affiliation:

1. Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC

2. Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan, ROC

3. Department of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC

4. Department of Computer Science and Information Management, Providence University, Shalu, Taichung Hsien 433, Taiwan, ROC

5. Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, Taiwan, ROC

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 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 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.

Publisher

World Scientific Pub Co Pte Lt

Subject

Computer Science Applications,Molecular Biology,Biochemistry

Link

https://www.worldscientific.com/doi/pdf/10.1142/S0219720003000095

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