Complexity of Multiple Sequence Alignment
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چکیده
It is shown that the multiple alignment problem with SP-score is NP-hardforeachscoringmatrixinabroadclassM that includes most scoring matrices actually used in biological applications. The problem remains NP-hard even if sequences can only be shifted relative to each other and no internal gaps are allowed. It is also shown that there is a scoring matrix M 0 such that the multiple alignment problem for M 0 is MAX-SNP-hard, regardless of whether or not internal gaps are allowed.hardness, polynomial time approximation scheme. 1. Introduction The importance of good multiple sequence alignment algorithms is evidenced by the large number of programs that have been developed for this task (Fasman and Salzberg 1998). Finding an optimal alignment of k sequences appears to quickly become computationally intractable as k increases. For example, dynamic programming algorithms that are guaranteed to nd a best scoring alignment of k sequences with mean length n have a running time of O(n k) (Carillo and Lipman 1988). This explains the widespread use of heuristic algorithms for multiple alignment. It has been formally proved by Wang and Jiang (1994) and Bonizzoni and Della Vedova (2000) that there are scoring matrices for which the problem of nding a multiple
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تاریخ انتشار 1999