Algorithms for Loosely Constrained Multiple Sequence Alignment

  • Bin Song
  • Feng-feng Zhou
  • Guo-liang Chen
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3314)

Abstract

For finding accurate and biologically meaningful multiple sequence alignment, it is required to consider a loosely constrained version of multiple sequence alignment. This paper is the first to define a loosely constrained multiple sequence alignment (LCMSA). And it also designs a complete algorithm for the loosely constrained pair-wise sequence alignment problem with the time complexity of O((α + 1)n2(α + 1)) and an approximation algorithm for LCMSA running in time O(k2(α + 1)n2(α + 1)), k and n is the number and the maximum length of input sequences, and α is the length of constrained sequence. In fact, α is small compared to n and it is reasonable to regard it as a constant. So, the former two algorithms run in polynomial time. Finally, a LCMSA software system is built up.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Jiang, T., Xu, Y., Zhang, M.Q.: Current Topics in Computational Molecular Biology. The MIT Press, Cambridge (2002)Google Scholar
  2. 2.
    Gusfield, D.: Efficient Methods for Multiple Sequence Alignment with Guaranteed Error Bounds. Bulletin of Mathematical Biology 55, 141–154 (1993)MATHGoogle Scholar
  3. 3.
    Tang, C.Y., Lu, C.L., Chang, M.D.-T., Tai, Y.-T., Sun, Y.-J., Chao, K.-M., Chang, J.-M., Chiou, Y.-H., Wu, C.-M., Chang, H.-T., Chou, W.-I.: Constrained Multiple Sequence Alignment Tool Development and Its Application to RNase Family Alignment. In: Proceeding of the first IEEE Computer Society Bioinformatics Conference, pp. 127–137 (2002)Google Scholar
  4. 4.
    Chin, F.Y.L., Ho, N.L., Lam, T.W., Wong, P.W.H., Chan, M.Y.: Efficient Constraint Multiple Sequence Alignment with Performance Guarantee. In: Proceeding of the second IEEE Computer Society Bioinformatics Conference, pp. 337–346 (2003)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Bin Song
    • 1
  • Feng-feng Zhou
    • 1
  • Guo-liang Chen
    • 1
  1. 1.Department of Computer Science and TechnologyUniversity of Science and Technology of ChinaHefeiP. R. China

Personalised recommendations