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AL2CO: calculation of positional conservation in a protein sequence alignment.

J Pei1, N V Grishin

  • 1Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA.

Bioinformatics (Oxford, England)
|August 29, 2001
PubMed
Summary

We developed a program to calculate conservation indices for protein sequence alignments. This tool helps identify important protein regions and improve alignment accuracy.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Amino acid sequence alignments are crucial for analyzing protein structure, function, and evolution.
  • Conserved positions in alignments often indicate functional or structural importance, while poorly conserved regions may signal alignment errors.
  • Quantifying conservation with indices aids motif detection and visualization of spatial conservation features.

Purpose of the Study:

  • To develop a computational tool for calculating conservation indices in multiple sequence alignments.
  • To assess the utility of conservation indices for motif detection, alignment quality assessment, and refinement.

Main Methods:

  • Developed a program (AL2CO) to compute conservation indices using various methods, including unweighted and weighted frequencies.

Related Experiment Videos

  • Implemented entropy-based, variance-based, and matrix score-based approaches to define conservation.
  • Calculated indices for over 35,000 positions across 284 alignments from the SMART database.

    • Main Results:

    • Different methods for calculating conservation indices yielded highly correlated results (correlation coefficient > 0.85).
    • Conservation indices showed significant correlation between adjacent positions, with a window of three positions optimal for motif detection.
    • Positions with gaps exhibited lower conservation properties compared to other positions.

    Conclusions:

    • Conservation indices are a valuable tool for assessing multiple sequence alignment quality.
    • The developed methods can aid in the objective function for refining multiple sequence alignments.
    • The AL2CO program is freely available for use in protein sequence analysis.