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GraphDNA: a Java program for graphical display of DNA composition analyses.

Jamie M Thomas1, Daniel Horspool, Gordon Brown

  • 1Department of Microbiology and Biochemistry, University of Victoria, Victoria, BC, V8W 3P6, Canada. jmthomas@uvic.ca <jmthomas@uvic.ca>

BMC Bioinformatics
|January 25, 2007
PubMed
Summary
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GraphDNA visualizes DNA nucleotide composition, revealing local asymmetries within sequences. This tool aids in characterizing viral genomes like poxviruses and coronaviruses.

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • DNA sequences exhibit local deviations from equal nucleotide composition (A=T, G=C).
  • Intra-strand nucleotide distribution analysis is crucial for understanding genome organization and processes.
  • Graphical methods have been developed to analyze these nucleotide distribution patterns.

Purpose of the Study:

  • To introduce GraphDNA, a user-friendly Java application for visualizing DNA nucleotide composition.
  • To enable direct comparison of multiple DNA sequences through graphical representations.

Main Methods:

  • GraphDNA accepts standard sequence file formats (GenBank, EMBL, FASTA).
  • The software generates and displays multiple graphical representations of DNA skews and walks.

Related Experiment Videos

  • It allows for the visualization of multiple sequences simultaneously in a single window.

    • Main Results:

    • GraphDNA provides a simple interface for visualizing DNA nucleotide composition.
    • The tool facilitates the characterization of viral genomes, such as poxviruses and coronaviruses, using DNA skews.
    • Multiple sequence comparisons are enabled through simultaneous plotting.

    Conclusions:

    • GraphDNA is a platform-independent, Open Source tool for analyzing nucleotide trends in DNA.
    • It supports various input formats and allows for comprehensive visualization of sequence data.