C. Tang, C. Lu, M. Chang, Yin-Te Tsai, Yuh-Ju Sun, K. Chao, Jia-Ming Chang, Yu-Han Chiou, Chia-Mao Wu, Hao-Teng Chang, Wei-I Chou
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Constrained multiple sequence alignment tool development and its application to RNase family alignment
In this paper, we design an algorithm of computing a constrained multiple sequence alignment (CMSA) 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 a, then the time-complexity of our CMSA algorithm for aligning K sequences is /spl Oscr/(/spl alpha/Kn/sup 4/), 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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