Study of Codon Degeneracy Based on Similarity Measure

Abstract

In genetics, Codon degeneracy is a salient feature which refers to a single amino acid being encoded by more than one codon. According to a study, Degeneracy of genetic code helps an organism to prosper on earth. Each amino acid is encoded by triplet codes of four possible (Guanine (G), Adenine (A), Cytosine (C), or Thymine (T/U)) bases. The genetic codon degeneracy occurs mainly due to the variance in third position e.g. the amino acids Glycine is encoded by four codons GGU, GGC, GGA, GGG differ only in third base. Taking part of more than one tri nucleotides sequence out of 64 triplets to encode one amino acids lead to the concept of Degeneracy. In this manuscript we formulate a new classifying technique with the help of cosine similarities to explain the degeneracy. Further we have done a comparison of our method with an existing classification technique. The consequences of our results open a new paradigm to study the genetics from a new mathematical perspective. The disassortative nature of codons networks may help us to understand the flow of genetic information in the evolution process of amino acids.