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

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11 Author(s)
Chuan Yi Tang ; Dept. of Comput. Sci., Nat. Tsing Hua Univ., Hsinchu, Taiwan ; Chin Lung Lu ; Hao-Teng Chang ; Yin-Te Tsai
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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 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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Bioinformatics Conference, 2002. Proceedings. IEEE Computer Society

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