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DISTAN--a program which detects significant distances between short oligonucleotides.

A K Konopka1, G W Smythers

  • 1National Institutes of Health, Laboratory of Mathematical Biology, Frederick, MD 21701.

Computer Applications in the Biosciences : CABIOS
|September 1, 1987
PubMed
Summary
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Oligonucleotide frequencies in DNA follow a Yule distribution.

Computers & chemistry·1996

This study introduces a novel algorithm for analyzing oligonucleotide distances in DNA sequences. The findings reveal distinct sequence periodicities in protein-coding regions, introns, and repeated DNA, offering insights into their biological functions.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Understanding DNA sequence composition and organization is crucial for deciphering gene function and regulation.
  • Oligonucleotide frequencies and their spatial distribution provide insights into DNA structure and evolutionary pressures.

Purpose of the Study:

  • To develop and apply an algorithm for detecting distances between oligonucleotides in large nucleic acid sequence collections.
  • To analyze sequence periodicities in different DNA categories (eukaryotic exons, bacterial genes, introns, repeated DNA).

Main Methods:

  • Development of an algorithm to calculate ratios of observed to expected oligonucleotide frequencies at specific distances.
  • Analysis of four distinct DNA sequence categories: eukaryotic exons, bacterial genes, introns, and non-Alu repeated DNAs.

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  • Identification of periodic occurrence patterns for mono-, di-, and trinucleotides.

    • Main Results:

    • Protein-coding regions (eukaryotic exons, bacterial genes) exhibit characteristic three-base periodicities for mononucleotides and dinucleotides, independent of reading frame.
    • A majority of trinucleotides, including stop signals, also show three-base periodicity in coding regions.
    • Mirror-symmetric trinucleotides (excluding GCG, CGC) display two-base periodicity in introns.
    • Specific two- and three-base periodic motifs were identified in repeated DNAs.

    Conclusions:

    • The observed sequence periodicities suggest distinct functional roles and evolutionary constraints in different DNA regions.
    • Three-base periodicity in coding regions likely relates to codon usage and protein synthesis efficiency.
    • Two-base periodicity in introns and motifs in repeated DNA may indicate specific structural or regulatory functions.