AUTOMATIC DISPLAY OF RNA SECONDARY STRUCTURES

A set of programs written in C language with the GL library and under UNIX has been developed for generating compact, pleasant and non-overl apping displays of secondary structures of ribonucleic acids. The firs t program, rnasearch, implements a new search procedure that dynamical ly, rearranges overlapping portions of the two-dimensional drawing whi le preserving clear and readable displays of the two-dimensional struc ture. The algorithm is fast (the execution time for the command rnasea rch is 38.6 s for the 16S rRNA of Escherichia coli with 1542 bases), a ccepts 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-dimensio nal structure by using the program print2D which builds a Postscript f ile. Moreover the two-dimensional drawing can be labelled for represen ting data coming from chemical modifications and/or enzymatic cleavage s. Application to a few secondary structures such as RNaseP, 5S rRNA a nd 16S rRNA are given.