title: Automatic display of RNA secondary structures.
abstract: 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 s for 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.
authors.affiliation: UPR Structure des Macromolécules Biologues et Mécanismes de Reconnaissance, Institut de Biologie Moléulaire et Cellulaire du CNRS, Strasbourg, France.
authors.forename: G
authors.initials: G
authors.lastname: Muller
authors.forename: C
authors.initials: C
authors.lastname: Gaspin
authors.forename: A
authors.initials: A
authors.lastname: Etienne
authors.forename: E
authors.initials: E
authors.lastname: Westhof
mesh_terms: D000465:Algorithms; D001412:Bacillus subtilis / Q000737:chemistry / Q000235:genetics; D001483:Base Sequence; D003196:Computer Graphics; D004722:Endoribonucleases / Q000235:genetics; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics; D029968:Escherichia coli Proteins; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics; D016337:RNA, Catalytic / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics; D012341:RNA, Ribosomal, 5S / Q000737:chemistry / Q000235:genetics; D043262:Ribonuclease P; D012984:Software
chemical_list: D029968:Escherichia coli Proteins; D012329:RNA, Bacterial; D016337:RNA, Catalytic; D012336:RNA, Ribosomal, 16S; D012341:RNA, Ribosomal, 5S; D012313:RNA; D004722:Endoribonucleases; D043262:Ribonuclease P; C470865:ribonuclease P, E coli