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Plot Rna Secondary Structure Data Into Image

Hi to all,

I obtained a secondary structure file predicted from a non-coding rna. I am giving a portion of it , I want to convert this data into RNA image. Are there any webservers available to upload this text file and convert into an image for better visualization.

   >2D
   ::::::[[[[[[[[[[[[,<<______________________>>,,,,,,,,,,,,,((
   CGAGUCAACUGGGCAGUCGCCGCUUCG--------CGAGAAGGGGAGGAAAGUCCGGGCU

thank you raghul

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updated by Biostar Biostar • written by Raghul Raghul

For some reason, the portion that you posted is not formatted properly (not your fault, problem with this site).

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written by Neilfws Neilfws

2 answers

How about RNAplot it's a command line tool or RNAfold server, but that takes the sequence, not the shape data. Or why not make a RNA movie?

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written by Michael Dondrup Michael Dondrup

Try centroidfold: http://www.ncrna.org/centroidfold/ or mfold http://mfold.rna.albany.edu/?q=mfold/ Alternatively you can download vienna RNA modeling package. You can just google for the url.

This website compares/benchmark the secondary structure prediction servers: http://iimcb.genesilico.pl/comparna/

• 121 views • link
written by Pappu Pappu

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