Non-approximability of weighted multiple sequence alignment


Manthey, Bodo (2003) Non-approximability of weighted multiple sequence alignment. Theoretical Computer Science, 296 (1). pp. 179-192. ISSN 0304-3975

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Abstract:We consider a weighted generalization of multiple sequence alignment (MSA) with sum-of-pair score. MSA without weights is known to be $N P$-complete and can be approximated within a constant factor, but it is unknown whether it has a polynomial time approximation scheme. Weighted multiple sequence alignment (WMSA) can be approximated within a factor of O(log2n) where n is the number of sequences.

We prove that WMSA alignment is MAX$\mathcal{S N P}$-hard and establish a numerical lower bound on its approximability, namely $\frac{324}{323}-\in $. This lower bound is obtained already for the simple binary weighted case where the weights are restricted to 0 and 1. Furthermore, we show that WMSA and its restriction to binary weights can be approximated to the same degree.
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Copyright:© 2003 Elsevier
Electrical Engineering, Mathematics and Computer Science (EEMCS)
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