How to highlight regions in RNA second structure

Question

[biolab]

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!

[Asaf]

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.

Answer 1

[shzhang]

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).