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SQUARE--determining reliable regions in sequence alignments.

Michael L Tress1, Osvaldo Graña, Alfonso Valencia

  • 1CNB-CSIC, Calle Darwin, Cantoblanco, 28049 Madrid, Spain. mtress@gredos.cnb.uam.es

Bioinformatics (Oxford, England)
|February 7, 2004
PubMed
Summary
This summary is machine-generated.

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The Server for Quick Alignment Reliability Evaluation (SQUARE) predicts reliably aligned residues in sequence alignments. This web tool aids researchers in assessing sequence alignment quality using structural profile databases.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Sequence alignments are crucial for understanding protein function and evolution.
  • Assessing the reliability of residue alignments is essential for accurate biological interpretation.
  • Existing methods may lack user-friendly interfaces or efficient prediction capabilities.

Purpose of the Study:

  • To present the Server for Quick Alignment Reliability Evaluation (SQUARE), a web-based tool.
  • To enable prediction of reliably aligned residues in protein sequence alignments.
  • To provide researchers with a reliable method for evaluating sequence alignment quality.

Main Methods:

  • SQUARE utilizes a database of profiles from sequences with known 3D structures.

Related Experiment Videos

  • It calculates alignment scores for each residue based on these profiles.
  • The server provides a graphical output of alignment scores and reliability indicators.

    • Main Results:

    • SQUARE successfully predicts regions of reliably aligned residues.
    • The tool offers graphical visualization of alignment reliability scores.
    • Scores can be compared with secondary structure, conserved residues, and functional sites.

    Conclusions:

    • SQUARE is an effective web-based tool for evaluating sequence alignment reliability.
    • It enhances the interpretation of sequence alignments by identifying trustworthy residue mappings.
    • The server facilitates more accurate downstream analyses in bioinformatics and structural biology.