如何可视化生成的 RNA 二级结构
我正在开发一种可视化 RNA 二级结构的工具，为此我实现了 Nussinov 算法，该算法将 RNA 二级结构生成为具有相应索引的列表，代码可以在此处找到 [0]
但我真的坚持理解如何将其可视化（作为平面图），这上面的代码为我提供了二级结构的顺序列表，所以有人可以建议我如何可视化该结构。可以在此处找到此类工具的示例 [1]
[1] http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi
我知道有更好的算法，但目前我只想用这个进行可视化，一旦我理解了可视化，我就会寻求更好的算法。
I'm working on a tool to visualize RNA secondary structure, for this purpose I have implemented Nussinov's algorithm which generates the RNA secondary structure as list with the corresponding indices, the code can be found here [0]
But I really stuck with understanding how I should visualize it (as a planar graph), the code above gives me a sequential list of the secondary structure, so can someone please suggest me as to how I can visualize the structure.An example of such tool can be found here [1]
[1] http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi
and I know there are better algorithms but for now I would just want to visualize with this and once I understand visualization, I will go for a better algorithm.
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通过算法可视化 RNA 的二级结构（或任何图形）是一个难题。您需要注意尽可能减少重叠，同时保持一致的链接长度。正如其他答案所指出的，您已经可以使用许多现有的实现。我将添加另一个非常易于使用且无需下载的程序：
forna - nibiru。 tbi.univie.ac.at/forna
在这里，您只需输入点括号字符串：
这将为您提供如下所示的可视化效果：
这是使用 ViennaRNA RNAplot 程序和 d3 的力导向图算法的组合来计算的。
Visualizing the secondary structure of RNA (or any graph, for that matter) algorithmically is a difficult problem. You need to take care that there are as few overlaps as possible while maintaining consistent link lengths. As the other answers have pointed out, there are a number of existing implementations that you can already use. I'll just throw in another one that's quite easy to use and requires no downloads:
forna - nibiru.tbi.univie.ac.at/forna
Here you just need to enter a dotbracket string:
This will give you a visualization that looks something like this:
This is computed using a combination of the ViennaRNA RNAplot program and d3's force-directed graph algorithm.
您可以使用 jmol 来做到这一点。 Jmol 允许您使用其 java 或者我相信它的 javascript api 向坐标空间添加任意键/原子。
当然，一般来说，此类数据将使用 PDB 文件格式。
You could do this with jmol . Jmol allows you to add arbitrary bonds / atoms to a coordinate space using its java or I believe its javascript api also.
In general, of course, PDB file formats would be used for such data.
RNAviz 很旧，但仍然常用。 JalView 显然去年应该通过 GSoC 项目获得 RNA 二级结构渲染，但我不确定是什么程序中的状态是。
RNAviz is old but still commonly used. JalView apparently was supposed to get RNA secondary structure rendering thru a GSoC project last year, but I'm not sure what the status in the program is.