RNA2Drawer: geometrically strict drawing of nucleic acid structures with graphical structure editing and highlighting of complementary subsequences
RNA2Drawer: geometrically strict drawing of nucleic acid structures with graphical structure editing and highlighting of complementary subsequences
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DOI：
10.1080/15476286.2019.1659081
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发表时间：
2019-08-26
期刊：
影响因子：
4.1
通讯作者：
Simon, Anne E.
中科院分区：
文献类型：
--
作者：
Johnson, Philip Z.;Kasprzak, Wojciech K.;Simon, Anne E.
RNA结构预测程序仍然不完善，许多子结构仍然通过人工探索来识别，这在RNA结构绘制程序中进行最有效。然而，大多数核酸结构绘制程序的结构修饰能力有限（即，在碱基之间断裂并形成新的键），通常需要对结构符号进行文本编辑。RNA2Drawer的开发是为了允许图形结构编辑，同时保持绘图的几何形状（例如，椭圆环、具有均匀堆叠的碱基对的茎）。此外，该程序允许注释，例如碱基的着色和圈出以及三级相互作用的绘制（例如，伪结）。RNA2Drawer还可以绘制通常需要的元件，例如可选的扁平化最外环，并通过自动突出显示互补序列来辅助结构编辑，这有助于发现潜在的新的和替代的配对，特别是长距离的三级配对，这在许多RNA病毒的基因组中是生物学上至关重要的，并且无法通过当前的结构预测程序准确预测。此外，RNA2Drawer将绘图输出为PNG文件或PPTX和SVG文件，使得绘图的每个对象（例如，bonds）是一个单独的PPTX或SVG对象，允许在Microsoft PowerPoint或矢量图形编辑器（如Adobe Illustrator）中进行进一步操作。PowerPoint是演示文稿的标准，通常用于为出版物创建图形，而RNA2Drawer是第一个将图形导出为PPTX文件的程序。
RNA structure prediction programs remain imperfect and many substructures are still identified by manual exploration, which is most efficiently conducted within an RNA structure drawing program. However, most nucleic acid structure drawing programs have limited capability for structure modification (i.e., breaking and forming new bonds between bases), often requiring that the structure notation be textually edited. RNA2Drawer was developed to allow for graphical structure editing while maintaining the geometry of a drawing (e.g., ellipsoid loops, stems with evenly stacked base pairs) throughout structural changes and manual adjustments to the layout by the user. In addition, the program allows for annotations such as colouring and circling of bases and drawing of tertiary interactions (e.g., pseudoknots). RNA2Drawer can also draw commonly desired elements such as an optionally flattened outermost loop and assists structure editing by automatically highlighting complementary subsequences, which facilitates the discovery of potentially new and alternative pairings, particularly tertiary pairings over long-distances, which are biologically critical in the genomes of many RNA viruses and cannot be accurately predicted by current structure prediction programs. Additionally, RNA2Drawer outputs drawings either as PNG files, or as PPTX and SVG files, such that every object of a drawing (e.g., bases, bonds) is an individual PPTX or SVG object, allowing for further manipulation in Microsoft PowerPoint or a vector graphics editor such as Adobe Illustrator. PowerPoint is the standard for presentations and is often used to create figures for publications, and RNA2Drawer is the first program to export drawings as PPTX files.