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A structure-based method for protein sequence alignment.

Maricel G Kann1, Paul A Thiessen, Anna R Panchenko

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA.

Bioinformatics (Oxford, England)
|December 23, 2004
PubMed
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We introduce SALTO, a tool aligning protein sequences to PSSMs using structural information for improved accuracy. SALTO offers performance comparable or superior to existing methods, with an explicit gapping model for protein families.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Bioinformatics

Background:

  • Protein sequence data is rapidly growing, necessitating advanced comparison tools.
  • Position-specific scoring matrices (PSSMs) capture conserved patterns in protein families.
  • Current PSSM methods often miss crucial structural information.

Purpose of the Study:

  • Introduce Structure-based ALignment TOol (SALTO) for protein sequence alignment.
  • Integrate structural information into PSSM-based sequence comparison.
  • Improve sensitivity and accuracy in identifying related protein sequences.

Main Methods:

  • SALTO aligns protein query sequences to PSSMs.
  • Utilizes rules for gap placement and scoring consistent with conserved domain alignments.

Related Experiment Videos

  • Employs an explicit gapping model tailored to each protein family.

    • Main Results:

    • SALTO's alignment scores typically follow an extreme value distribution.
    • Achieves performance similar to or better than existing tools like IMPALA.
    • Provides accurate alignments and identifies related sequences effectively.

    Conclusions:

    • SALTO enhances protein sequence comparison by incorporating structural insights.
    • The explicit gapping model offers an advantage for family-specific alignments.
    • SALTO is available as a stand-alone program and integrated into Cn3D.