We consider the problem of aligning a set of sequences subject to a given constrained sequence, which has applications in computational biology. In this paper we show that sequence alignment for two sequences A and B with a given distance function and a constrained sequence of k identical characters (say character c) can be solved in O( min {kn 2,(t - k)n 2}) time, where n is the length of A and B, and t is the minimum number of occurrences of character c in A and B. We also prove that the problem of constrained center-star sequence alignment (CCSA) is NP-hard even over the binary alphabet. Furthermore, for some distance function, we show that no polynomial-time algorithm can approximate the CCSA within any constant ratio. © 2014 Springer International Publishing.
CITATION STYLE
Zhang, Y., Chan, J. W. T., Chin, F. Y. L., Ting, H. F., Ye, D., Zhang, F., & Shi, J. (2014). On the complexity of constrained sequences alignment problems. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8497 LNCS, pp. 309–319). Springer Verlag. https://doi.org/10.1007/978-3-319-08016-1_28
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