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Related Experiment Videos

COMPASS server for remote homology inference.

Ruslan I Sadreyev1, Ming Tang, Bong-Hyun Kim

  • 1Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA. sadreyev@chop.swmed.edu

Nucleic Acids Research
|May 23, 2007
PubMed
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The COMPASS web server offers enhanced homology detection and alignment construction using multiple sequence alignments (MSAs). This tool improves sensitivity, alignment completeness, and speed for protein analysis.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Homology detection and local alignment are crucial for understanding protein function and structure.
  • The COMPASS method previously required local installation, limiting accessibility.
  • Existing tools may have limitations in sensitivity, alignment quality, or speed.

Purpose of the Study:

  • To introduce a new web server for the COMPASS method, enhancing accessibility and usability.
  • To present an updated version of COMPASS with improved performance characteristics.
  • To demonstrate the utility of the COMPASS web server for protein structure-function prediction.

Main Methods:

  • Development of a web server for the COMPASS homology detection and alignment construction method.

Related Experiment Videos

  • Utilizing multiple sequence alignments (MSAs) to derive numerical profiles.
  • Performing local profile-profile alignments and analytical E-value estimation.

    • Main Results:

    • The new COMPASS web server offers increased sensitivity and selectivity in homology detection.
    • The server generates longer and more complete local alignments.
    • Computational speed is significantly enhanced compared to previous versions.
    • A user-friendly interface with intuitive parameter control and flexible output is provided.

    Conclusions:

    • The COMPASS web server provides a powerful and accessible tool for homology detection and protein analysis.
    • The enhanced features facilitate the identification of distant homologs for uncharacterized protein families.
    • This tool aids in protein structure-function prediction and broader biological research.