2003•Journal of Bioinformatics and Computational BiologyRequires access

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

Chuan Yi Tang, Chin Lung Lu, Margaret Dah‐Tsyr Chang, Yin-Te Tsai, Yuh-Ju Sun, Kun‐Mao Chao, Jia‐Ming Chang, Yu-Han Chiou, Chia-Mao Wu, Hao‐Teng Chang, Wei-I Chou

Open publisher page 53 citations

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 alpha, then the time-complexity of our CMSA algorithm for aligning K sequences is O(alphaKn(4)), 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.

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Key concepts: Multiple sequence alignment, Sequence (biology), Heuristic, RNase P, Sequence alignment, Computer science, Structural alignment, Function (biology)