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.
Chapter PDF
Similar content being viewed by others
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
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.
Josse J., Kaiser A.D. and Kornberg A., 1961, J. Biol. Chem. 236: 864–875.
Karlin S. and Burge C., 1995, Dinucleotide relative abundance extremes: a genomic signature, Trends in Genetics 11:283–290.
Karlin S., Ladunga I. and Blaisdell B.E., 1994, Heterogeneity of genomes: measures and values, Proc. Natl. Acad. Sci. USA 91: 12837–12841.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1998 Springer Science+Business Media New York
About this chapter
Cite this chapter
Tobler, K., Ackermann, M. (1998). Comparison of the Di- and Trinucleotide Frequencies from the Genomes of Nine Different Coronaviruses. In: Enjuanes, L., Siddell, S.G., Spaan, W. (eds) Coronaviruses and Arteriviruses. Advances in Experimental Medicine and Biology, vol 440. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-5331-1_104
Download citation
DOI: https://doi.org/10.1007/978-1-4615-5331-1_104
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4613-7432-9
Online ISBN: 978-1-4615-5331-1
eBook Packages: Springer Book Archive