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Related Experiment Videos

DicodonUse: the programme for dicodon bias visualization in prokaryotes.

J Paces1, V Paces

  • 1Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic. paces@img.cas.cz

Folia Biologica
|January 7, 2003
PubMed
Summary
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The DicodonUse program quickly assesses prokaryotic gene content using dicodon frequencies. It differentiates genuine genes from non-coding sequences and distinguishes native genes from horizontally acquired ones.

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Prokaryotic genome analysis requires accurate gene identification.
  • Distinguishing intrinsic genes from horizontally acquired genes is crucial for understanding genome evolution.
  • Existing methods for gene assessment can be time-consuming.

Purpose of the Study:

  • To develop a rapid and straightforward method for assessing gene content in prokaryotic nucleotide sequences.
  • To differentiate true genes from open reading frames (ORFs) that are not genes.
  • To distinguish between genes native to a genome and those acquired through horizontal gene transfer.

Main Methods:

  • Utilizing the DicodonUse program for sequence analysis.
  • Analyzing frequencies of dicodons (pairs of adjacent codons) specific to an organism.

Related Experiment Videos

  • Applying dicodon frequency profiles to identify gene structures and origins.

    • Main Results:

    • The DicodonUse program effectively identifies open reading frames.
    • It successfully distinguishes between genuine genes and non-gene ORFs.
    • The program accurately differentiates between intrinsic and acquired genes within prokaryotic genomes.

    Conclusions:

    • Dicodon frequency analysis provides a fast and simple method for prokaryotic gene assessment.
    • This approach aids in understanding genome composition and evolutionary history.
    • DicodonUse offers a valuable tool for genomic research.