Algorithms for Loosely Constrained Multiple Sequence Alignment

  • Bin Song
  • Feng-feng Zhou
  • Guo-liang Chen
Conference paper

DOI: 10.1007/978-3-540-30497-5_34

Part of the Lecture Notes in Computer Science book series (LNCS, volume 3314)
Cite this paper as:
Song B., Zhou F., Chen G. (2004) Algorithms for Loosely Constrained Multiple Sequence Alignment. In: Zhang J., He JH., Fu Y. (eds) Computational and Information Science. CIS 2004. Lecture Notes in Computer Science, vol 3314. Springer, Berlin, Heidelberg

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.

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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

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