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© Oxford University Press

Analysis of Gene Evolution: the software AGE

Didier G. Arquès , Christian J. Michel 1,3 and Karine Orieux 2

Université de Franche-Comié, Laboratoire d'Informatique de Besançon, Unité Associée CNRS No. 822, 16 route de Gray, F-25030 Besançon, France
1Friedrich Miescher Institut, Bioinformatic Group Mattenstrasse 22, PO Box 2543, CH-4002 Basel, Switzerland
2Universitéde Haute-Alsace, Laboratoire de Mathématique et Informatique, Faculté des Sciences et Techniques 4-rue des Frères Lumière, F-68093 Mulhouse, France

3Present address: Equipe de Biologie Théorique, Université de Franche-Comié, Institut Universitaire de Technologie de Belfort-Montbétard, BP 527, 90016 Belfort, France.

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)nucleot-ides, 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.

Received on January 21, 1991; accepted on June 6, 1991

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