Secondary Structure Prediction

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The length is different from sequence
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RNA structure prediction is powered by Fold tool in RNAstructure package. The structure score of the ith base can be converted to a pseudo-free energy according to this formula (Katherine et al.):

ΔGscore(i) = slope * ln[score(i)+1] + intercept

Users can manually enter the sequence and structure score to predict the secondary structure, or select the sequence from the transcipt summary page. Here is an example:

  1. Go to transcript summary page of ORF8 of SARS-CoV-2 (link)
  2. Scroll to Load probing data panel and select the dataset
    Load probing data
  3. After the structure score loaded, scroll to Sequence panel and select the first 100nt. Click the Predict button
    Select a region
  4. A new "Secondary Structure Prediction" page will pop up. The sequence and structure scores are filled in. Click the "Submit" button
    Secondary Structure Prediction
  5. Predicted structures are showed, users can visualize with forna or VARNA
    Predicted structures