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Statistical properties of open reading frames in complete genome sequences.

W Li1

  • 1Laboratory of Statistical Genetics, Rockefeller University, New York, NY 10021, USA. wli@linkage.rockefeller.edu

Computers & Chemistry
|July 15, 1999
PubMed
Summary

This study analyzes open reading frames (ORFs) in prokaryotic and yeast genomes, finding yeast chromosomes have more long ORFs. Base composition analysis reveals distinct patterns at different codon positions.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Open reading frames (ORFs) are crucial for gene identification and understanding genome organization.
  • Statistical analysis of ORF properties provides insights into genome evolution and function.
  • Previous studies have explored ORF characteristics, but comprehensive comparative analyses across diverse genomes are ongoing.

Purpose of the Study:

  • To statistically analyze the properties of open reading frames (ORFs) in complete prokaryotic and yeast genomes.
  • To investigate the influence of GC content on ORF size distribution.
  • To examine base composition asymmetry in ORFs between DNA strands and at codon positions.

Main Methods:

  • Analysis of seventeen prokaryotic and sixteen yeast chromosome sequences.

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  • Application of statistical techniques including quantile tables, QQ-plots, rank-size plots (Zipf's plots), and spatial densities.
  • Regression analysis to study base composition asymmetry.

    • Main Results:

    • Yeast chromosomes exhibit a tendency for more long ORFs compared to archaeal and eubacterial genomes.
    • No significant evidence was found to reject the null hypothesis of similar ORF distribution across six reading frames and two strands.
    • Distinct base composition patterns were observed: purine-rich (G- and A-rich) at the first codon position, co-existing A- and T-rich branches at the second, and weakly T-rich at the third.

    Conclusions:

    • Comparative genomic analysis reveals differences in ORF length distributions between yeast and prokaryotes.
    • ORF distribution is largely consistent across different reading frames and strands.
    • Codon position-specific base composition asymmetry is a conserved feature across analyzed genome sequences.