Constrained multiple sequence alignment tool development and its application to RNase family alignment.
Journal
Proceedings - IEEE Computer Society Bioinformatics Conference, CSB 2002
Pages
127-137
Date Issued
2002
Author(s)
Tang, Chuan Yi
Lu, Chin Lung
Chang M.D.-T.
Tsai, Yin-Te
Sun, Yuh-Ju
Chang, Jia-Ming
Chiou, Yu-Han
Wu, Chia-Mao
Chang, Hao-Teng
Chou, Wei-I.
Abstract
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.
Event(s)
1st International IEEE Computer Society Bioinformatics Conference, CSB 2002
Type
conference paper
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