The complexity of multiple sequence alignment with SP-score that is a metric
نویسندگان
چکیده
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.
منابع مشابه
Global Multiple Sequence Alignment
As with pairwise alignment, multiple sequence alignments (MSAs) are typically scored by assigning a score to each column and summing over the columns. The most common approach to scoring individual columns in a multiple alignment is to calculate a score for each pair of symbols in the column, and then sum over the pair scores. This is called sum-of-pairs or SP-scoring. For global multiple seque...
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عنوان ژورنال:
- Theor. Comput. Sci.
دوره 259 شماره
صفحات -
تاریخ انتشار 2001