Complimentary DNA sequence data analysis of prokaryotic systems

Complimentary DNA sequence data of Φ × 174, fd, f1, G4, Ml3, MS2, λ and T7 phages ofEscherichia coli are analysed at mono-, di-, tri- and tetranucleotide levels. Our analysis shows that, (i) mononucleotides have certain preferences to occur at specific positions X₁, X₂, X₃ of codon, (ii) These nucleotides interact nonlinearly to form dinucleotide and this dinucleotide also interacts nonlinearely with a third nucleotide to form codon, (iii) However, nonlinear interactions are negligible at tetranucleotide level suggesting that, coding regions of complimentary DNA are Markov chains of order two. Trinucleotide potential values in three frames have suggested that, at least thirteen different trinucleotides can be used as a marker to locate coding regions in DNA of prokaryotes. (iv) Parallel paired codons are expressed in such a way that one of the codons in the pair expresses with high frequency while the other with low frequency. On the other hand the complimentary codon pairs express with small frequency difference, (v) In the synonymous codon groups, codon ending with T are found to express with more frequency