A Simple Di-Nucleotide Based DNA Analysis Applied to Phylogeny of Mammals using Zinc Fingers

We have developed a simple algorithm of counting the probability of each possible type of di-nucleotide occurring in a DNA sequence to determining homologs and phylogeny between mammals. A 2-dimensional representation was developed for visualization. This method does not require any DNA alignment or for the DNA sequences to be of the same length. We applied our tools to determining homologs between related zinc finger structures, as well as determining mammalian phylogeny. We also demonstrate this method's ability to classifying dissimilar DNA sequences. Likely future work along these lines will be to increase our vector to include dimensions for other variables such as fractal dimension, large automated DNA searches, and segmenting the DNA sequence before calculating our vector in order to keep some position data.