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

Authors:
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
Affiliations:
-;-;-;-;-;-;-;-;-;-;-
Venue:
CSB '02 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Year:
2002

Citing 4
Cited 7

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Efficient Constrained Multiple Sequence Alignment with Performance Guarantee

CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
A fast algorithm for the constrained multiple sequence alignment problem

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Regular expression constrained sequence alignment

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Bit-Parallel Algorithm for the Constrained Longest Common Subsequence Problem

Fundamenta Informaticae
Algorithms for loosely constrained multiple sequence alignment

CIS'04 Proceedings of the First international conference on Computational and Information Science
Regular expression constrained sequence alignment

CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
Time and space efficient algorithms for constrained sequence alignment

CIAA'04 Proceedings of the 9th international conference on Implementation and Application of Automata

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Abstract

In this paper, we design an algorithm of computing a constraine 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 residuesneeded to be aligned together is a constant 驴, then the time-complexity of our CMSA algorithm for aligning K sequences is O (驴Kn4), 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.