User GuidesSnapGene User Guide RNAView Predicted RNA Secondary Structure

View Predicted RNA Secondary Structure

How do I view the predicted secondary structure of a single stranded RNA (ssRNA) sequence?

SnapGene 6.1 and later use the ViennaRNA package to calculate ssRNA secondary structure.

SnapGene can show predicted secondary structure for ssRNA sequences up to 3000 nucleotides in length.

Open a Single Stranded RNA Sequence

Open or import a single strand RNA (ssRNA) sequence.

If a sequence imports as DNA then convert it to RNA via menu Actions → Make RNA.

If a sequence imports as double strand RNA then convert to ssRNA via menu Actions → Convert to Single Stranded....

Switch to "Secondary Structure" View

Switch to "Secondary Structure" view.

Change the View

Move the pointer to the edge of the image to see the "rotation" cursor. Click and drag to rotate the structure.

Move the pointer to the center of the screen to see the "drag" cursor. Click and drag to move the structure.

Use the drop down to set the "move mode" to:

  • Default - Rotate or drag based on pointer position
  • Rotate - Set to Rotate mode only
  • Drag - Set to Drag mode only

Use the mouse scroll wheel to move the structure.

Use CTRL + mouse scroll wheel (windows, Linux), or Command + mouse scroll wheel (macOS), to zoom in or out.

Click the dropdown to resize the structure, or change the size of the "base" text.

Click on the value to type and enter a specific percentage zoom value.

View Information  About the Structure

The structure is colored based on estimated "Confidence". For paired bases, the color denotes the probability that the bases are paired. For unpaired regions the color denotes the probability of being unpaired. The "Confidence" legend is displayed in the top left corner of the window.

SnapGene displays the optimal predicted structure with the lowest calculated free energy.

The lower portion of the "Secondary Structure" panel shows information about the structure. Consult the Vienna package documentation for information on these values and how they are calculated.

Export the Structure

Click the "Export As..."  dropdown to export the structure as an image, or in "dot-bracket" notation.

Alternatively, right-click on the structure to show a contextual menu to Export, or to copy the structure image or dot bracket information to the clipboard for pasting into another program.