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© 1988 IRL Press Ltd

A secondary and tertiary structure editor for nucleic acids

Robert Cedergren , Daniel Gautheret , Guy Lapalme 1 and François Major 1

Départments de Biochimie, Université de Montréal C. P. 6128, Succursale A, Montréal, Quebéc, Canada, H3C 3J7
1d'Informatique et Recherche Opérationnelle. Université de Montréal C. P. 6128, Succursale A, Montréal, Quebéc, Canada, H3C 3J7

A major difficulty in the evaluation of secondary and tertiary structures of nucleic acids is the lack of convenient methods for their construction and representation. As a first step in a study of the symbolic representation of biopolymers, we report the development of a structure editor written in Pascal, permitting model construction on the screen of a personal computer. The program calculates energies for helical regions, allows user-defined helices and displays the secondary structure of a nucleic acid based on a user-selected set of helices. Screen and printer outputs can be in the form of a backbone or the letters of the primary sequence. The molecule can then be displayed in a format which simulates its three-dimensional structure. Using appropriate glasses, the molecule can be viewed on the screen in three dimensions. Other options include the manipulation of helices and single-stranded regions which results in changes in the spatial relationship between different regions of the molecule. The editor requires an IBM or compatible PC, 640 kbyte memory and a medium or high resolution graphics card.

Received on September 19, 1987; accepted on November 15, 1987

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