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A Maximum Weighted Path Approach to Multiple Alignments for DNA Sequences

  • Hongwei Huo
  • Vojislav Stojkovic
  • Zhiwei Xiao
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4222)

Abstract

This paper presents a novel approach, called MWPAlign Maximum Weighted Path approach to multiple ALIGNment, to perform global multiple alignment of DNA sequences. In our method, de Bruijn graph is used to describe input sequences information. As a result, a consensus-finding problem can be transformed to a maximum weighted path problem of the graph. MWPAlign gets almost linear computation speed of multiple sequences alignment problem. Experimental results show that the proposed algorithm is feasible, and for large number of sequences with lower mutation rate 5.2%, MWPAlign generates better alignment and has a lower computation time as compared to CLUSTALW, T-Coffee and HMMT.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Hongwei Huo
    • 1
  • Vojislav Stojkovic
    • 2
  • Zhiwei Xiao
    • 1
  1. 1.School of Computer Science and TechnologyXidian UniversityXi’anChina
  2. 2.Department of Computer ScienceMSUBaltimoreUSA

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