Analysis of gene evolution: the software AGE.

Abstract

The software AGE (Analysis of Gene Evolution) has been developed both to study a genetic reality, i.e. the identification of statistical properties in genes (e.g. periodicities), and to simulate this observed genetic reality, by models of molecular evolution. AGE has two types of models: (i) models of sequence creation from oligonucleotides: concatenation model in series of an oligonucleotide, independent (or Markov) mixing model of oligonucleotides according to given probabilities (or a Markov matrix); (ii) models of sequence evolution from created sequences: insertion/deletion process of (mono,di,tri)nucleotides, base mutation process. The study of a reality and the development of simulation models are based on several new algorithms: approximated simulation and exact calculus to compute various autocorrelation functions, Fourier transformation of autocorrelation curves, recognition of a curve form, etc. AGE is implemented on IBM or compatible microcomputers and can be used by biologists without any computer knowledge to identify statistical properties in their newly determined DNA sequence and to explain them by models of molecular evolution.