Investigations of oligonucleotide usage variance within and between prokaryotes.

PLoS Computational Biology
Jon BohlinDavid W Ussery

Abstract

Oligonucleotide usage in archaeal and bacterial genomes can be linked to a number of properties, including codon usage (trinucleotides), DNA base-stacking energy (dinucleotides), and DNA structural conformation (di- to tetranucleotides). We wanted to assess the statistical information potential of different DNA 'word-sizes' and explore how oligonucleotide frequencies differ in coding and non-coding regions. In addition, we used oligonucleotide frequencies to investigate DNA composition and how DNA sequence patterns change within and between prokaryotic organisms. Among the results found was that prokaryotic chromosomes can be described by hexanucleotide frequencies, suggesting that prokaryotic DNA is predominantly short range correlated, i.e., information in prokaryotic genomes is encoded in short oligonucleotides. Oligonucleotide usage varied more within AT-rich and host-associated genomes than in GC-rich and free-living genomes, and this variation was mainly located in non-coding regions. Bias (selectional pressure) in tetranucleotide usage correlated with GC content, and coding regions were more biased than non-coding regions. Non-coding regions were also found to be approximately 5.5% more AT-rich than coding regions, on av...Continue Reading

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Citations

Aug 25, 2009·Genome Biology·Gregory J DickJillian F Banfield
Dec 4, 2009·PloS One·Jon Bohlin, Eystein Skjerve
Mar 31, 2010·PloS One·Colin F Davenport, Burkhard Tümmler
Aug 10, 2010·BMC Genomics·Jon BohlinDavid W Ussery
Nov 4, 2010·BMC Bioinformatics·David R Kelley, Steven L Salzberg
Oct 20, 2010·Bioinformatics·Vetriselvi Rangannan, Manju Bansal
Mar 17, 2012·Science·Adam AutonGil McVean
Jan 26, 2010·Photosynthesis Research·Colin DavenportBurkhard Tümmler
Jan 24, 2009·Environmental Microbiology·Colin F DavenportBurkhard Tümmler
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Jan 19, 2018·Nucleic Acids Research·Pawel S KrawczykAndrzej Dziembowski
Dec 6, 2017·PeerJ·Sajia AkhterRobert A Edwards
Sep 15, 2021·Epigenetics : Official Journal of the DNA Methylation Society·Matthieu BruneauxTarmo Ketola

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