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Align-m--a new algorithm for multiple alignment of highly divergent sequences.

Ivo Van Walle1, Ignace Lasters, Lode Wyns

  • 1Department of Ultrastructure, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium. ivwalle@vub.ac.be

Bioinformatics (Oxford, England)
|February 14, 2004
PubMed
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Align-m improves multiple sequence alignment for highly divergent sequences. This new tool offers comparable or better accuracy than existing methods, significantly reducing incorrect alignments.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiple sequence alignment of divergent sequences is computationally challenging.
  • Existing methods often suffer from inaccurate scoring functions or inefficient search heuristics.
  • Accurate alignment is crucial for understanding evolutionary relationships and protein function.

Purpose of the Study:

  • Introduce Align-m, a novel program for multiple sequence alignment.
  • Address the limitations of current algorithms in handling highly divergent sequences.
  • Improve the accuracy and efficiency of global sequence alignment.

Main Methods:

  • Utilizes a non-progressive local approach to guide global alignment.
  • Developed and tested using two extensive datasets covering the entire SCOP classification.

Related Experiment Videos

  • Evaluated performance against established algorithms like ClustalW, T-Coffee, and DiAlign.

    • Main Results:

    • Align-m demonstrates comparable or superior accuracy in correctly aligning residues, particularly for distantly related sequences.
    • Significantly reduces the number of incorrectly aligned residues compared to other tested algorithms (over 15% difference on average).
    • Performance validated on sequence similarities ranging from 0 to 50% identity.

    Conclusions:

    • Align-m offers a robust solution for multiple sequence alignment of divergent sequences.
    • The program provides higher accuracy and fewer errors, especially in challenging evolutionary scenarios.
    • Align-m is available for public use, facilitating advancements in bioinformatics research.