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GeneViTo: visualizing gene-product functional and structural features in genomic datasets.

Georgios S Vernikos1, Christos G Gkogkas, Vasilis J Promponas

  • 1Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 15701, Athens, Greece. gverniko@yahoo.gr

BMC Bioinformatics
|November 5, 2003
PubMed
Summary

GeneViTo is a JAVA-based workbench for genome-wide analysis, enabling interactive exploration and visualization of genomic data. This tool aids in assessing analysis algorithms and supports in-depth genomic studies by comparing annotation and prediction data.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Increasing genomic sequence data necessitates advanced computational methods for automated genome annotation and comparative genomics.
  • Effective visualization tools are crucial for exploring raw bioinformatics data and analysis results.
  • Visual inspection aids in assessing analysis algorithm quality and facilitates in-depth genomic studies.

Purpose of the Study:

  • To develop a JAVA-based application, GeneViTo, for interactive genome-wide analysis and visualization.
  • To provide a workbench for integrating and comparing diverse genomic and proteomic data.
  • To facilitate the evaluation of genome annotation and prediction data.

Main Methods:

  • GeneViTo utilizes a Graphical User Interface (GUI) for interactive data extraction and visualization.

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  • The application processes DNA and protein sequences from public or proprietary sources.
  • It integrates meta-data from prediction algorithms, classification schemes, and user-defined features.

    • Main Results:

    • GeneViTo offers a workbench for genome-wide analysis through visual interaction.
    • It allows easy extraction of genomic and proteomic data, including sequence features and structural/functional information.
    • The tool facilitates comparison between annotation and prediction data, aiding in cases of poor annotation or for evaluating predictions.
    • High-quality JPEG image files can be generated for further scientific use.

    Conclusions:

    • GeneViTo provides an inspectional view of genomic functional elements from both database annotations and analysis tools.
    • It supports the overall analysis of existing genomes by integrating diverse data sources.
    • The application is compatible with Linux and Windows operating systems with a Java Runtime Environment.