Non-approximability of Weighted Multiple Sequence Alignment

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

Abstract

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(log2n) 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.

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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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