------------------------------------------------------ UMR 5558 ---------------- Author(s) : G. PERRIERE, J.R. LOBRY and J. THIOULOUSE Correspondence discriminant analysis: a multivariate method for comparing classes of protein and nucleic acid sequences. Computer Applications in the Biosciences Serial Number : Publishing agreement. Key-Words : Correspondence discriminant analysis, proteins subcellular location, leading and lagging coding sequences, prokaryotic genomes. Abstract We present here two applications of a multivariate method suited for studying classes of nucleotide or protein sequences: correspondence discriminant analysis. The first example of use is a discrimination of Escherichia coli proteins according to their subcellular location (membrane, cytoplasm and periplasm). Due to the good resolution of the method, it is possible to predict the subcellular location of E.coli proteins when this information is not known. The second example is a discrimination between coding sequences from leading and lagging strands in four bacterial species: Mycoplasma genitalium, Haemophilus influenzae, E.coli and Bacillus subtilis. The programs used for computing the analysis are integrated in a publicly available package that runs on MacOS 7.x or Windows 95 operating systems (http://biomserv.univ-lyon1.fr/ADE-4.html). These programs are also accessible through our World Wide Web server (http://biomserv.univ-lyon1.fr/NetMul.html). E-Mail : thioulou@biomserv.univ-lyon1.fr Laboratoire de Biometrie, Genetique et Biologie des Populations (UMR 5558) - Univ. C. Bernard LYON I - 69622 VILLEURBANNE CEDEX