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Parametric alignment of ordered trees.

Lusheng Wang1, Jianyun Zhao

  • 1Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, Peoples Republic of China. lwang@cs.cityu.edu.hk

Bioinformatics (Oxford, England)
|November 25, 2003
PubMed
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We developed a parametric tool for aligning ordered trees, enabling users to visualize parameter effects on alignments. This tool offers efficient computation and reduced memory usage for tree comparison applications.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Bioinformatics

Background:

  • Tree similarity computation is vital for RNA secondary structures, genetics, and chemical analysis.
  • Parametric tools for sequence alignment exist, but a similar tool for ordered trees is needed.
  • Current tree alignment methods lack user control over parameter weighting.

Purpose of the Study:

  • To develop a parametric tool for aligning two ordered trees.
  • To allow users to observe the impact of parameter choices on tree alignment outcomes.
  • To provide a practical solution for the need of user-adjustable tree alignment.

Main Methods:

  • Developed a parametric tool for ordered tree alignment.
  • Designed an efficient algorithm for tree alignment incorporating gap penalties.

Related Experiment Videos

  • Optimized the algorithm's space complexity.

    • Main Results:

    • The developed tool enables explicit visualization of parameter choice effects on optimal tree alignments.
    • The algorithm achieves an efficient time complexity of O(n(2)deg(2)).
    • Space complexity was reduced from O(n(2)deg(2)) to O(n log n. deg(2)).

    Conclusions:

    • The new parametric tool facilitates a deeper understanding of ordered tree alignment parameters.
    • The efficient algorithm and reduced space complexity make tree alignment more practical.
    • This work addresses the need for user-centric tools in tree comparison applications.