The effect of DNA phase structure on DNA walks

Abstract:

We have performed several kinds of DNA walks which often are the first steps for further analysis of DNA structure and long range correlations. The DNA walks analysing frequency of G+C versus A+T cannot indicate the coding strand while purine versus pyrimidine DNA walks or two-dimensional (A-T,G-C) DNA walks in some instances can indicate the coding strand but cannot resolve the coding frame. The modified two-dimensional (A-T,G-C) DNA walks respecting the three-nucleotide codon structure show very high correlation in nucleotide composition of DNA coding sequences. They can distinguish between coding and non-coding sequences and indicate the strand and the phase in which DNA is coding.