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© Oxford University Press

Automatic display of RNA secondary structures

G. Muller 1, Ch. Gaspin 1,2, A. Etienne 1 and E. Westhof 1,3

1UPR Structure des Macro,nolécules Biologiques et Mécanismes de Reconnaissance, Equipe de Modélisation rt de Simulation des Acides Nucléiques, Institut de Biologie Moléculaire er Cellulaire du CNRS 15 rue René Descartes, 67084 Strasbourg Cedex France
2Station de Biométrie et d 'Intelligence Artificielle, Institut National de la Recherche Agronomique Chemin de Borde-Rouge, Auzeville BP 27, 31 326 C Cedex, France

3To whom reprint requests should be sent

A set of programs written in C language with the GL library and under UNIX has been developed for generating compact, pleasant and non-overlapping displays of secondary structures of ribonucleic acids. The first program, rnasearch, implements a new search procedure that dynamically rearranges overlapping portions of the two-dimensional drawing while preserving clear and readable displays of the two-dimensional structure. The algorithm is fast (the execution time for the command rnasearch is 38.6 sfor the 16S rRNA of Escherichia coli with 1542 bases), accepts outputs from two-dimensional prediction programs and therefore allows for rapid comparison between the various two-dimensional folds generated. A second program, rnadisplay, allows the graphical display of the computed two-dimensional structures on a graphics workstation. Otherwise, it is possible to obtain a paper output of the two-dimensional structure by using the program print2D which builds a Postscript file. Moreover the two-dimensional drawing can be labelled for representing data coming from chemical modifications and/or enzymatic cleavages. Application to a few secondary structures such as RNaseP, 5S rRNA and 16S rRNA are given.

Received on December 7, 1992; accepted on March 25, 1993

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