A secondary and tertiary structure editor for nucleic acids.

R Cedergren; D Gautheret; G Lapalme; F Major

doi:10.1093/bioinformatics/4.1.143

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A secondary and tertiary structure editor for nucleic acids.

R Cedergren·D Gautheret·G Lapalme·F Major

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Abstract

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.

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Algorithms Base Sequence Computer Graphics Models, Molecular Nucleic Acid Conformation RNA, Transfer Software Thermodynamics Journal Article Research Support, Non-U.S. Gov't

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R Cedergren, D Gautheret, G Lapalme, F Major. 1988. A secondary and tertiary structure editor for nucleic acids.. https://doi.org/10.1093/bioinformatics%2F4.1.143

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