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