RNAcanvas: interactive drawing and exploration of nucleic acid structures.
RNAcanvas: interactive drawing and exploration of nucleic acid structures.
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DOI：
10.1093/nar/gkad302
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发表时间：
2023-07-05
影响因子：
14.9
通讯作者：
中科院分区：
文献类型：
--
作者：
核酸结构的二维绘制，特别是RNA结构的绘制，是核酸研究交流的基础。然而，对于数千个核苷酸长的结构，手工绘制结构是费力和不可行的。RNAcanvas自动将残基排列成形状严格的茎和环，同时提供强大的交互编辑功能，包括点击并拖动布局调整。绘制的元素以点击的方式高度可定制，包括颜色、字体、大小和阴影、灵活的编号以及基本轮廓。第三级相互作用可以绘制为可拖动的曲线。完全支持用于描述非正则碱基对的Leontis-Westhof符号，以及用于结构特征(例如发夹)的文本标签。RNAcanvas还具有许多针对大型结构的独特功能和性能优化，这些功能和性能优化无法正确预测，需要基于研究人员自己的分析和专业知识进行手动改进。为此，RNAcanvas具有点击式结构编辑功能，实时突出互补序列和基序搜索功能，这些新功能极大地有助于识别假定的远程三级相互作用、局部结构的从头分析和系统发育比较。为了便于制作出版物质量的图形，图形可以同时以SVG和PowerPoint格式导出。网址：https://rnacanvas.app.探索RNAcanvas中2,692个核苷酸的柑橘黄脉相关病毒基因组结构。当前选定的序列突出显示为黄色。RNAcanvas突出显示了两个假定的第三配对紫色(光标悬停)和粉色。
Two-dimensional drawing of nucleic acid structures, particularly RNA structures, is fundamental to the communication of nucleic acids research. However, manually drawing structures is laborious and infeasible for structures thousands of nucleotides long. RNAcanvas automatically arranges residues into strictly shaped stems and loops while providing robust interactive editing features, including click-and-drag layout adjustment. Drawn elements are highly customizable in a point-and-click manner, including colours, fonts, size and shading, flexible numbering, and outlining of bases. Tertiary interactions can be drawn as draggable, curved lines. Leontis-Westhof notation for depicting non-canonical base-pairs is fully supported, as well as text labels for structural features (e.g. hairpins). RNAcanvas also has many unique features and performance optimizations for large structures that cannot be correctly predicted and require manual refinement based on the researcher's own analyses and expertise. To this end, RNAcanvas has point-and-click structure editing with real-time highlighting of complementary sequences and motif search functionality, novel features that greatly aid in the identification of putative long-range tertiary interactions, de novo analysis of local structures, and phylogenetic comparisons. For ease in producing publication quality figures, drawings can be exported in both SVG and PowerPoint formats. URL: https://rnacanvas.app. Exploring the 2,692 nt citrus yellow vein-associated virus genome structure in RNAcanvas. Currently selected sequence highlighted yellow. RNAcanvas has highlighted two putative tertiary pairings purple (hovered by cursor) and pink.
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影响因子：
16
作者：
Ziv O;Price J;Shalamova L;Kamenova T;Goodfellow I;Weber F;Miska EA
通讯作者：
Miska EA
DOI：
10.1093/bioinformatics/btp250
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Darty K;Denise A;Ponty Y
通讯作者：
Ponty Y
影响因子：
5.8
作者：
Byun, Yanga;Han, Kyungsook
通讯作者：
Han, Kyungsook
影响因子：
3.7
作者：
Shabash, Boris;Wiese, Kay C.
通讯作者：
Wiese, Kay C.
影响因子：
5.8
作者：
Wiegreffe, Daniel;Alexander, Daniel;Zeckzer, Dirk
通讯作者：
Zeckzer, Dirk