The complexity of multiple sequence alignment with SP-score that is a metric (2001)
| Venue: | TCS |
| Citations: | 17 - 0 self |
BibTeX
@ARTICLE{Bonizzoni01thecomplexity,
author = {Paola Bonizzoni and Gianluca Della Vedova},
title = {The complexity of multiple sequence alignment with SP-score that is a metric},
journal = {TCS},
year = {2001},
volume = {259},
pages = {2001}
}
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Abstract
This paper analyzes the computational complexity of computing the optimal alignment of a set of sequences under the SP (sum of all pairs) score scheme. We solve an open question by showing that the problem is NP -complete in the very restricted case in which the sequences are over a binary alphabet and the score is a metric. This result establishes the intractability of multiple sequence alignment under a score function of mathematical interest, which has indeed received much attention in biological sequence comparison.
Citations
| 8880 | Computers and Intractability: A Guide to the Theory of NPCompleteness - Garey, Johnson - 1979 |
| 505 | Optimization, approximation, and complexity classes - Papadimitriou, Yannakakis - 1988 |
| 177 | Jiang T: On the complexity of multiple sequence alignment - Wang - 1994 |
| 89 | Efficient methods for multiple sequence alignment with guaranteed error bounds - Gusfield - 1993 |
| 62 | A survey of multiple sequence comparison methods - Chan, Wong, et al. - 1992 |
| 48 | Mapping the genome: Some combinatorial problems arising in molecular biology - Karp - 1993 |
| 47 | Approximations algorithms for multiple sequence alignment - Bafna, Lawler, et al. - 1994 |
| 3 | Letter to the editor: Commentary on the letter by - Fitch - 1993 |
| 3 | A simplified proof of the np- and max snp-hardness of multiple sequence tree alignment - Wareham - 1995 |
| 3 | Letter to the Editor: The Triangle Inequality and character - Wheeler - 1993 |
| 2 | The multiple sequence alignment in biology - Carrillo, Lipman - 1988 |
