Non-approximability of weighted multiple sequence alignment
نویسندگان
چکیده
منابع مشابه
Non-approximability of Weighted Multiple Sequence Alignment
We consider a weighted generalization of multiple sequence alignment with sumof-pair score. Multiple sequence alignment without weights is known to be NPcomplete and can be approximated within a constant factor, but it is unknown whether it has a polynomial time approximation scheme. Weighted multiple sequence alignment can be approximated within a factor of O(log n) where n is the number of se...
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We prove that the multiple sequence alignment problem with weighted sum-of-pairs score is APX-hard for arbitrary metric scoring functions over the binary alphabet. This holds even when the weights are restricted to zero and one.
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An algorithm for progressive multiple alignment of sequences with insertions " , 1. Introduction The problem of sequence alignment is to find the patterns of sequence conservation and similarity between pairs or sets of given sequences. In biological contexts, similarity between biological sequences usually amounts to either functional or structural similarities or divergence from a common ance...
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Given two sequences S1, S2 and a constrained sequence C, the longest common subsequence of S1, S2 with restriction to C is defined as the constrained longest common subsequence (CLCS) of S1, S2 and C. At the same time, the best alignment of S1, S2 with restriction to C is defined as the constrained pairwise sequence alignment (CPSA) of S1, S2 and C. Previous algorithms have shown that both CLCS...
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Multiple sequence alignments are an essential tool for protein structure and function prediction, phylogeny inference and other common tasks in sequence analysis. Recently developed systems have advanced the state of the art with respect to accuracy, ability to scale to thousands of proteins and flexibility in comparing proteins that do not share the same domain architecture. New multiple align...
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ژورنال
عنوان ژورنال: Theoretical Computer Science
سال: 2003
ISSN: 0304-3975
DOI: 10.1016/s0304-3975(02)00439-5