Constrained multiple sequence alignment tool development and its application to RNase family alignment
Resource
Journal of Bioinformatics and Computational Biology,1,267-287.
Journal
Journal of bioinformatics and computational biology
Journal Volume
1
Journal Issue
2
Pages
267-287
Date Issued
2003-03
Date
2003-03
Author(s)
Tang, Chuan Yi
Lu, Chin Lung
Chang, Margaret Dah-Tsyr
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 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.
Other Subjects
ribonuclease; algorithm; amino acid sequence; article; chemistry; classification; comparative study; computer program; evaluation; methodology; molecular genetics; sequence alignment; sequence analysis; sequence homology; validation study; Algorithms; Amino Acid Sequence; Molecular Sequence Data; Ribonucleases; Sequence Alignment; Sequence Analysis, Protein; Sequence Homology, Amino Acid; Software
Type
journal article