Question: How to highlight regions in RNA second structure
0
gravatar for biolab
2.6 years ago by
biolab1.2k
biolab1.2k wrote:

Dear All,

I have many miRNA precursor sequences, and it is easy to get the pictures of their secondary structures in batch using RNAFOLD, MFOLD or other tools. My problem is: how to highlight or label a region (for example, miRNA or miRNA*) in the RNA structure graph by customized color?

Thank you very much for your suggestions!

rna second structure • 869 views
ADD COMMENTlink modified 9 months ago by shzhang10 • written 2.6 years ago by biolab1.2k

I did it some long time ago with Vienna package. They have a script to paint RNA structure according to some measure, I changed the script to read custom input.

ADD REPLYlink written 2.6 years ago by Asaf8.4k
1
gravatar for shzhang
9 months ago by
shzhang10
Australia
shzhang10 wrote:

Although it is quite a late reply, I think it is good if others need this.

forna (http://rna.tbi.univie.ac.at/forna/) provides an easy way to highlight regions in RNA secondary structure. You can specify any region and colour scheme to highlight the region you are interested in. By selescting Colors > Color Scheme > Set to specify the region and colour (e.g. 15-35:pink to highlight the region from the 15th to 35th nucleotides in pink).

ADD COMMENTlink modified 9 months ago • written 9 months ago by shzhang10
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