GENOME ANALYSIS FOR NUCLEOTIDE INTERACTIONS IN FULLY SEQUENCED GENOMES OF SELECTIVE PROKARYOTES

Fully sequenced prokaryotic genomes of Escherichia coli, Haemophilus i nfluenzae and Methanococcus janaschii were subjected to genome analysi s for nucleotide interactions. The analysis was restricted to inter-nu cleotide relations like two nucleotides in a dinucleotide, three nucle otides in a codon and two codons in a dicon. This relational analysis was carried out in C language and was compiled on a C++ compiler. The relational analysis showed a preferential dinucleotide frequency (the observed frequencies of AA and TT were higher than the expected freque ncy and the observed frequencies of CC and GG). From codon frequency d istribution analysis, sub-codonic elements have been noticed, exerting that the first one or first two nucleotide may reasonably determine t he next nucleotide(s) in a codon. The analysis further reveals the exi stence of short-range randomness or chaotic behaviour in prokaryotic g enomes, which might be a forerunner for the origin of introns in eukar yotes, besides being involved in a regulatory role.