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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
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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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AlgorithmsAmino Acid SequenceMolecular Sequence DataRibonucleasesSequence AlignmentSequence Analysis, ProteinSequence Homology, Amino AcidSoftwareComparative StudyEvaluation StudyJournal ArticleResearch Support, Non-U.S. Gov'tValidation Study

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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. 2003. Constrained multiple sequence alignment tool development and its application to RNase family alignment.. https://doi.org/10.1142/s0219720003000095

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