How do I view the predicted secondary structure of a single stranded nucleotide sequence?
SnapGene 6.1 and later use the ViennaRNA package to calculate ssRNA secondary structure.
SnapGene can show predicted secondary structure for single stranded RNA (ssRNA) sequences up to 3000 nucleotides in length.
SnapGene 7.1 and later can show predicted secondary structure for single stranded DNA (ssDNA) sequences up to 3000 nucleotides in length.
Open a Single Stranded RNA or DNA Sequence
Open, import or create an ssRNA or ssDNA sequence.
If a sequence imports as DNA then you can convert it to RNA via menu Actions → Make RNA. Similarly, If a sequence imports as RNA then you can convert it to DNA via menu Actions → Make DNA.
If a sequence imports as double strand RNA or DNA then convert to ssRNA or ssDNA via menu Actions → Convert to Single Stranded....
Switch to "Secondary Structure" View
Switch to "Secondary Structure"† view.
† Note that the "Secondary Structure" View will only be available if your sequence is single stranded and less than 3000 nucleotides in length.
View a Predicted Structure
The right panel shows the top 10 structures predicted by ViennaRNA, ordered from lowest predicted free energy (1) to highest (10). Use the scroll bar to view all structures. Click on any structure to display it in the viewer.
View or Change the Calculation Settings
Click the "View and edit calculation parameters" button in the side toolbar to view the settings used to calculate the displayed structures. Consult the ViennaRNA package documentation for details on the use of these settings.
Adjust settings and click Recalculate to recalculate all structures.
Show or Hide Sequence Coordinates
In the side toolbar, toggle the "Show base index labels on structure" button to show or hide the 5' and 3' end labels and sequence coordinates.
Change the Mode
Click the dropdown to change between Select (S), Drag (D) or Rotate (R) modes. Alternatively type the associated hot-keys (s, d or r, respectively) to quickly switch between modes.
Select Sequence Mode
In "Select" mode, click to select a single nucleotide, then shift-click to select a nucleotide range.
Switch to Map or Sequence view to see the corresponding selected sequence region.
In "Drag" mode click and drag to move the structure.
Use the mouse scroll wheel to move the structure.
In "Rotate" mode, click and drag to rotate the structure.
Change the Structure Size
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.
Click "Zoom to Fit" to automatically scale to fit within the window.
Use CTRL + mouse scroll wheel (Windows, Linux), or Command + mouse scroll wheel (macOS), to zoom in or out.
View Information About the Structure
A "Confidence" legend is displayed in the top left corner of the window. The predicted 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 lower portion of the "Secondary Structure" panel shows information about the selected structure and ensemble. Consult the ViennaRNA package documentation for information on these values and how they are calculated.
Export a Structure
Click the "Export As..." dropdown to export the structure as an image, or in "dot-bracket" notation.
Alternatively, right-click in the viewer 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.