Name
Title | ||
|---|---|---|
Constrained multiple sequence alignment tool development and its application to RNase family alignment |
Abstract | ||
|---|---|---|
In this paper, we design an 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 (alphaKn4), 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. |
Year | DOI | Venue |
|---|---|---|
2002 | 10.1109/CSB.2002.1039336 | Proceedings / IEEE Computer Society Bioinformatics Conference. IEEE Computer Society Bioinformatics Conference |
Keywords | Field | DocType |
constraine multiple sequence alignment,constrained multiple sequence alignment,particular residue,rnase family alignment,time-complexity,cmsa algorithm,user-specified constraints,aligning k sequence,user-specified constraint,computing algorithm,rnase sequences,biology computing,rnase sequence,molecular biophysics,computational complexity,cmsa software system,rna molecule,constrained multiple sequence alignment tool development,rna molecule degradation catalysis,tool development,degradation,algorithm design and analysis,sequences,software systems,computer science,application software,rna,dynamic programming,time complexity,multiple sequence alignment,satisfiability | Structural alignment,Alignment-free sequence analysis,Computer science,Molecular biophysics,Bioinformatics,Multiple sequence alignment,RNase P,Computational complexity theory | Conference |
Volume | Issue | ISSN |
1 | 2 | 1555-3930 |
ISBN | Citations | PageRank |
0-7695-1653-X | 33 | 1.92 |
References | Authors | |
7 | 11 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Chuan Yi Tang | 1 | 704 | 79.25 |
| Chin Lung Lu | 2 | 423 | 34.59 |
| Margaret Dah-Tsyr Chang | 3 | 88 | 8.87 |
| Yin-Te Tsai | 4 | 143 | 13.27 |
| Yuh-ju Sun | 5 | 38 | 2.61 |
| Kun-mao Chao | 6 | 838 | 94.05 |
| Jia-Ming Chang | 7 | 141 | 10.75 |
| Yu-han Chiou | 8 | 38 | 2.61 |
| Chia-Mao Wu | 9 | 39 | 2.97 |
| Hao-Teng Chang | 10 | 115 | 11.04 |
| Wei-I Chou | 11 | 42 | 3.89 |