Perochon-Dorisse J, Chetouani F, Aurel S, Iscolo N, Michot B
Institut de Biologie Cellulaire et Génétique du CNRS, Toulouse, France.
Comput Appl Biosci. 1995 Feb;11(1):101-9. doi: 10.1093/bioinformatics/11.1.101.
RNA-d2 is a user-friendly program developed for interactively 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 of structural 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.
RNA-d2是一个用户友好型程序，用于交互式生成美观且不重叠的RNA二级结构绘图。它的设计目的是使绘图能够以非常自然和直观的方式进行编辑，以便强调几个分子之间的结构同源性，以及根据新数据更新碱基对集的折叠本身。该程序会自动生成一个多边形显示，其中未配对的核苷酸规则地位于圆圈上，茎在其周边和谐分布。RNA二级结构可以通过键盘进行编码，但该程序也能自动从热力学预测程序中绘制输出文件。用户根据编辑功能直接在不同的屏幕显示上进行交互。在彩色主链视图上执行任何子域的旋转/平移和茎的删除操作，以便更轻松地识别结构特征，而在完整的多边形视图上实现新碱基配对的添加和编号操作。每次修改都会实时显示在屏幕上。当尽管有主链视图的颜色编码，但显示仍被大量重叠遮挡时，自动功能会逐渐拉直由非常不对称的内部环高度压缩的子域。RNA-d2允许轻松解开和编辑长度超过1000个核苷酸的RNA分子。
