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LALNVIEW: a graphical viewer for pairwise sequence alignments

L Duret1, E Gasteiger, G Perrière

  • 1Department of Medical Biochemistry, University of Geneva, Switzerland. duret@dim.hcuge.ch

Computer Applications in the Biosciences : CABIOS
|December 1, 1996
PubMed
Summary
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LALNVIEW is a graphical tool for visualizing local sequence alignments. It displays sequence features alongside alignments, linking homology to structure and function.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Analyzing local sequence alignments is crucial for understanding protein and nucleic acid relationships.
  • Visualizing sequence features alongside alignments aids in functional and structural interpretation.

Purpose of the Study:

  • To introduce LALNVIEW, a graphical program for visualizing local sequence alignments.
  • To enable the display of sequence features within alignment visualizations.
  • To facilitate the connection between sequence homology and biological function/structure.

Main Methods:

  • Graphical visualization of local alignments between two sequences (protein or nucleic acids).
  • Representation of sequences using colored rectangles to depict similarities.

Related Experiment Videos

  • Automatic extraction and display of sequence features from database annotations (SWISS-PROT, GenBank, EMBL, HOVERGEN) via web servers.

    • Main Results:

    • LALNVIEW provides a visual overview of sequence similarities.
    • Sequence features such as exons, introns, active sites, and domains are displayed.
    • Web server integration allows automatic feature display from major sequence databases.

    Conclusions:

    • LALNVIEW is a valuable tool for analyzing pairwise sequence alignments.
    • The program effectively links sequence homology to known structural and functional information.
    • Freely available executables enhance accessibility for researchers on various platforms.