Non-approximability of Weighted Multiple Sequence Alignment

  • Bodo Siebert
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2108)


We consider a weighted generalization of multiple sequence alignment with sum-of-pair score. Multiple sequence alignment without weights is known to be NP-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 can be approximated within a factor of O(log2 n) where n is the number of sequences.

We prove that weighted multiple sequence alignment is MAX SNP-hard and establish a numerical lower bound on its approximability, namely 324/323 - €. 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 weighted multiple sequence alignment and its restriction to binary weights can be approximated exactly to the same degree.


Polynomial Time Multiple Sequence Alignment Weighted Score Optimal Alignment Polynomial Time Approximation Scheme 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2001

Authors and Affiliations

  • Bodo Siebert
    • 1
  1. 1.Institut für Theoretische InformatikMed. Universität zu LübeckLübeckGermany

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