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Comparison of the Di- and Trinucleotide Frequencies from the Genomes of Nine Different Coronaviruses

  • Kurt Tobler
  • Mathias Ackermann
Chapter
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 440)

Abstract

As an alternative to protein alignments for the comparison of sequences, the reiterations of mono- di- and trinucleotide frequencies were used for the comparison of Coronavirus sequences. The relative abundance of the di- and trinucleotide frequencies within the 3′ part from nine Coronavirus genomes were determined.

The patterns of dinucleotide frequencies and the trinucleotide frequencies showed some common features for all coronaviruses but also differences between the groups formerly defined on the base of antigenic relatedness.

The normalised dinucleotide frequencies were further used to calculate the distances between coronavirus sequences. Based on the dinucleotide frequency distances, coronaviruses can be divided into two groups which roughly reflect the taxonomic groups. In this kind of evaluation, however, IBV occupies a position different to the one that it would take based on most protein sequence comparisons. Based on similarities within coding sequences and antigenic properties IBV occupies a place outside of both groups. Based on the dinucleotide frequencies IBV gained a position in between of the TGEV-related and the MHV-clustered coronaviruses.

Keywords

Antigenic Relatedness Amino Acid Sequence Comparison Dinucleotide Frequency Human Coronavirus Transmissible Gastroenteritis Virus 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Burge C., Campbell A.M. and Karlin S., 1992, Over- and under-representation of short oligonucleotides in DNA sequences, Proc. Natl. Acad. Sci. USA 89: 1358–1362.PubMedCrossRefGoogle Scholar
  2. Josse J., Kaiser A.D. and Kornberg A., 1961, J. Biol. Chem. 236: 864–875.PubMedGoogle Scholar
  3. Karlin S. and Burge C., 1995, Dinucleotide relative abundance extremes: a genomic signature, Trends in Genetics 11:283–290.PubMedCrossRefGoogle Scholar
  4. Karlin S., Ladunga I. and Blaisdell B.E., 1994, Heterogeneity of genomes: measures and values, Proc. Natl. Acad. Sci. USA 91: 12837–12841.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 1998

Authors and Affiliations

  • Kurt Tobler
    • 1
  • Mathias Ackermann
    • 1
  1. 1.Institute of Virology, Vet.-med. FacultyUniversity of ZurichZurichSwitzerland

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