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Application of DNA Fingerprinting using the D1S80 Locus in Lab Classes
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Published on: July 17, 2021

Two common profiles exist for genomic oligonucleotide frequencies.

Shang-Hong Zhang1, Lei Wang

  • 1Key Laboratory of Gene Engineering of Ministry of Education, and Biotechnology Research Center, Sun Yat-sen University, Guangzhou, 510275, China. lsszsh@mail.sysu.edu.cn

BMC Research Notes
|November 20, 2012
PubMed
Summary

Genomic oligonucleotide frequencies exhibit two common profiles, linked to GC content and strand symmetry. These factors significantly influence genome evolution across diverse life forms.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Evolution

Background:

  • Previous studies identified a majority profile for trinucleotide frequencies in genomes.
  • Further research revealed two common trinucleotide frequency profiles, but their origins were unclear.
  • The applicability of these profiles to other oligonucleotide lengths remained undetermined.

Purpose of the Study:

  • To investigate genomic oligonucleotide frequency profiles beyond trinucleotides.
  • To explore the origins and characteristics of common genomic compositional profiles.
  • To determine the influence of GC content and strand symmetry on these profiles.

Main Methods:

  • Analysis of 571 prokaryotic genomes and selected eukaryotic nuclear genomes.
  • Examination of compositional features across various genetic systems.
  • Correlation analysis between genomic profiles and random sequence models with controlled GC content and symmetry.

Main Results:

  • Two distinct common profiles for genomic oligonucleotide frequencies were identified.
  • One profile corresponds to low-GC content genomes, the other to high-GC content genomes.
  • Both profiles strongly correlate with random sequences of equivalent GC content and first-order symmetry.

Conclusions:

  • Genomic GC content variations are a primary driver for the observed oligonucleotide frequency profiles.
  • Strand symmetry in genomic sequences also contributes significantly to these profiles.
  • GC content and strand symmetry are crucial factors shaping genome evolution.