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Related Experiment Videos

Detecting alien genes in bacterial genomes.

J Mrázek1, S Karlin

  • 1Department of Mathematics, Stanford University, California 94305-2125, USA.

Annals of the New York Academy of Sciences
|July 23, 1999
PubMed
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We developed new methods to calculate codon bias, identifying highly expressed and alien genes across various genomes. This approach helps distinguish essential genes from horizontally transferred ones, revealing insights into genome evolution.

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Codon bias is a non-random usage of synonymous codons.
  • Identifying highly expressed and horizontally transferred genes is crucial for understanding genome evolution and function.
  • Existing methods may not adequately differentiate gene origins and expression levels.

Purpose of the Study:

  • To present novel methods for calculating codon bias in gene groups and individual genes.
  • To enable the identification of highly expressed and alien genes within various genomes.
  • To provide a tool for analyzing gene transfer events and functional gene classes.

Main Methods:

  • Calculation of codon bias relative to a standard gene class.
  • Application of the method to diverse microbial genomes (yeast, bacteria, archaea).

Related Experiment Videos

  • Analysis of gene clusters to infer horizontal gene transfer events.

    • Main Results:

    • Successfully identified highly expressed genes (e.g., ribosomal proteins, elongation factors, photosystem II genes) and alien genes (e.g., ORFs of unknown function, transposases) in yeast, bacteria, and methanogens.
    • Demonstrated that nuclear ribosomal proteins in yeast are highly expressed, while mitochondrial ribosomal proteins appear alien.
    • Observed that alien genes frequently cluster, suggesting multi-gene transfer events.

    Conclusions:

    • The developed codon bias calculation methods are effective for distinguishing highly expressed and alien genes.
    • Codon bias analysis provides insights into gene origin, expression levels, and horizontal gene transfer.
    • The findings contribute to understanding genome composition and evolutionary dynamics in different organisms.