Constrained multiple sequence alignment tool development and its application to RNase family alignment

Author

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

Author_Institution

Dept. of Comput. Sci., Nat. Tsing Hua Univ., Hsinchu, Taiwan

fYear

2002

fDate

2002

Firstpage

127

Lastpage

137

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 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.

Keywords

biology computing; computational complexity; molecular biophysics; CMSA software system; RNA molecule degradation catalysis; RNase family alignment; RNase sequences; computing algorithm; constrained multiple sequence alignment tool development; time-complexity; user-specified constraints; Algorithm design and analysis; Application software; Bovine; Computer science; Degradation; Dynamic programming; Lungs; Pancreas; RNA; Sequences;

fLanguage

English

Publisher

ieee

Conference_Titel

Bioinformatics Conference, 2002. Proceedings. IEEE Computer Society

Print_ISBN

0-7695-1653-X

Type

conf

DOI

10.1109/CSB.2002.1039336

Filename

1039336