Molecular Informatics: Quantifying Information Patterns in the Genetic Code

Abstract

The Genetic Code appears to be a non-random triplet code in which both the position of a nucleotide within a codon, as well as its physicochemical nature, contribute to the identity of the expressed amino acid. The non-randomness of the code is manifested in apparent patterns in the mapping from codon to amino acid; some of the patterns seem quite clear, while other more subtle patterns are less obvious or certain. Discussion in the literature has been largely qualitative in nature. In this study, we employ evolution similarity data, widely employed in the field of bioinformatics, to explore the patterns relating nucleotide features to amino acids. The results support a hierarchical order based on position and physicochemical features proposed by Jimenez-Montaño et al., [“The Hypercube Structure of the Genetic Code Explains Conservative and Non-Conservative Amino Acid Substitutions in vivo and in vitro” Biosystems (1996) 39, pp. 117–125]. The method also provides a quantitative approach to testing the importance of other putative patterns.

Keywords:

• Genetic code
• Nucleotide
• Bioinformatics
• Amino acid