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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.

Published in:

Bioinformatics Conference, 2002. Proceedings. IEEE Computer Society

Date of Conference:

2002