Biological domain identification based in codon usage by means of rule and tree induction

Abstract

There are three domains in living nature: archaea, bacteria and eukarya. It has been shown, trough a number of multivariate tools, that codon usage, a 64 dimensional vector that stablishes how often a given organism makes use of each codon, is related to domain. Another method is proposed here based in rule and tree induction from codon usage of several organisms. It is shown that domain can be identified trough codon usage and a simple set of rules. Two methods were applied, CN2 and C4.5. Obtained rules describe data better than other methods, in the sense that are topological interpretable and have phenomenological meaning. © Springer-Verlag Berlin Heidelberg 2005.