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© Oxford University Press

RNA_d2: a computer program for editing and display of RNA secondary structures

J. Perochon-Dorisse , F. Chetouani 1, A. Aurel 2, N. Iscolo 1 and B. Michot 1,*

Institut de biologie Cellulaire et Geéneétique et Geéneétique du CNRS 118 route de Narbonne, 31062 Toulouse Cedex
1Laboratorie de Biologie Moleèculaire Eucaryote du CNRS. 118 route de Narbonne, 31062 Toulouse Cedex
2Station de Biomeétrie et Intelligence Artificielle, INRA, Chemin de Borde-Rouge BP 27, 31326 Castanent Tolosan Cedex, France

*Corresponding author (at USA)

RNA_d2 is a user–friendly program developed for inter–actively generating aesthetic and non–overlapping drawings of RNA secondary structures. It designed so that the drawings can be edited in a very natural and intuitive way, in order to emphasize structural homologies between several molecules, as well as the foldings themselves to update the base–pair sets according to new data. The program automatically produces a polygonal display in which the unpaired nucleotides are regularly positioned on circles and the stems harmoniously distributed on their periphery. RNA secondary structures can be encoded via the keyboard, but the program also automatically draws output files from thermodynamic prediction programs. The user interacts directly on different screen displays according to the editing functions. Rotation/translation of any subdomain and deletion of stems are performed on a coloured backbone view to make easier the identification ofstructural features, whereas addition of new base-pairings and numbering manipulation are realized on a complete polygonal view. Each modification is displayed in real time on the screen. When the display is obscured by numerous overlaps despite the colour code of the backbone view, an automatic function progressively straightens the subdomains which are highly compacted by very dissymmetric internal loops. RNA_d2 allows easy untangling and editing of RNA molecules > 1000 nucleotides long

Received on July 1, 1994; accepted on November 11, 1994

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