We used RNAplex for prediction of the RNA hybridization, but it returns the result in dot bracket format , and now we need the alignment format for further analysis, like which generated by mirnada, how to convert?
alignment format
ATA-AAC
| | |
GATGCG
The format with dots and brackets are used widely in RNA secondary structure. Basics - brackets means paired nucleotides, dots - nonpaired
Could you use this from your command line:
tr '.{}' ' ||' < yourInputFile > yourOutputFile
The software RNAplot from the Vienna package does exactly what you want. It takes the dot-bracket structure and produces an image showing alignments and loops.
You may also look at the posts related to the question "What RNA 2D structure viewer would you recommend?" here at RG.
Thank you all, though the suggested tools are not work for my purpose. The problem,at least partial,has been figured out by inhouse developed script.
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