Abstract
We consider the problem of aligning of k sequences of length n. The cost function is sum of pairs, and satisfies triangle inequality. Earlier results on finding approximation algorithms for this problem are due to Gusfield, 1991, who achieved an approximation ratio of 2 − 2/k, and Pevzner, 1992, who improved it to 2 − 3/k. We generalize this approach to assemble an alignment of k sequences from optimally aligned subsets of l<k sequences to obtain an improved performance guarantee. For arbitrary l<k, we devise deterministic and randomized algorithms yielding performance guarantees of 2−l/k. For fixed l, the running times of these algorithms are polynomial in n and k.
The research was supported in part by the National Science Foundation under grant CCR-9308567, the National Institute of Health under grant R01 HG00987 and the DOE grant DE-FG03-90ER60999.
Research supported in part by the DOE grant DE-FG03-90ER60999.
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© 1994 Springer-Verlag Berlin Heidelberg
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Bafna, V., Lawler, E.L., Pevzner, P.A. (1994). Approximation algorithms for multiple sequence alignment. In: Crochemore, M., Gusfield, D. (eds) Combinatorial Pattern Matching. CPM 1994. Lecture Notes in Computer Science, vol 807. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-58094-8_4
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DOI: https://doi.org/10.1007/3-540-58094-8_4
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