Other software

RNA secondary structure modeling

ShapeMapper does not perform structure modeling. To model RNA structures with SHAPE reactivity constraints, we recommend using the Fold module of RNAstructure for short sequences. Fold accepts a .fa sequence file and a .shape reactivity file as input, and produces a .ct file containing one or more modeled structures. For sequences longer than a few hundred nucleotides, we recommend using Superfold, which automates the process of running RNAstructure over subsequence windows and merging the resulting structures. Superfold accepts a .map file as input, and produces a .ct file containing a single predicted minimum free energy structure and a .dp file containing estimated base pairing probabilities.

RNA structure visualization

Arc diagrams

IGV

We recommend IGV for exploratory visualization of reactivity profiles and structure models for RNAs longer than a few hundred nucleotides. Once a .fa file is loaded as the reference sequence (Genomes → Load Genome from File), IGV can directly open .shape or .map reactivity profiles and .ct and .dp files generated by Superfold. To open these files, click File → Load from File, and click Continue if a dialog box pops up.

Traditional secondary structure diagrams

VARNA

VARNA is a user-friendly option for RNAs up to a few hundred nucleotides.

Pros:

  • Can directly open .ct files for visualization and adjustment.
  • Default layouts for short RNAs often require no manual adjustment
  • Intuitive layout adjustment

Cons:

  • Large structures often result in unmanageable layout overlaps.

Ribosketch

Ribosketch is a relatively new software package for RNA secondary structure visualization.

Pros:

  • Supports .ct files
  • Initial layouts for large RNAs often very good
  • Attractive publication-quality output images

Cons:

  • Manually editing larger structures can be somewhat cumbersome, especially if there are layout overlaps.

RNAstructure Structure Editor

Recent releases of RNAstructure include a fairly sophisticated graphical structure viewer/editor (the executable is named StructureEditor).

Pros:

  • Supports .ct files
  • Direct support for .shape reactivity coloring
  • Customizable nucleotide coloring for different publication styles

Cons:

  • Initial layouts are not very good
  • May require compiling from source

XRNA

For large RNAs, XRNA is often the only practical option to generate and edit publication-quality figures.

Pros:

  • Most comprehensive interface for manual layout adjustment

Cons:

  • Has not been updated since 2009
  • Non-intuitive interface
  • Does not support the .ct file format
  • Does not handle pseudoknotted structures well
  • May crash for very large RNAs
  • Vector output may be broken

How to load a .ct file:

As a workaround for XRNA's lack of .ct file support, RNAstructure can be used to open a .ct file and convert it to a helix text file that can be imported into XRNA. Run the graphical interface RNAstructureScript. Click File → Draw, and select a .ct file. Click Draw → Write Helix (Text) File.

In XRNA, click the Format tab. Click Format New Structure. Click New Primary Structure, and copy-paste in the RNA sequence, or click Read and select a text file containing only the RNA sequence. Close the dialog. Click Set New Helices → Read and select the helix text file created above. Close the dialog. Click Run Format to generate an initial layout, then move to the Edit tab for manual layout adjustment.

Alternatively, the pvclient.py wrapper script included with Superfold can be used to query the Pseudoviewer web service and generate a .xrna file that can be directly loaded by XRNA.

Coloring by SHAPE reactivity

Coloring secondary structure diagrams by SHAPE reactivity in an aesthetically pleasing, publication-quality format still often requires ad-hoc scripting. Some of these scripts may be included in future ShapeMapper releases. In the meantime, here we list steps to import ShapeMapper-generated reactivity profiles into several software packages and render with reasonably aesthetic color scales.

VARNA coloring

Right click → Color map → Show color map

Right click → Color map → Style → red

Right click → Color map → Load values → Choose file, and select a simplified reactivity profile (output by ShapeMapper) with a filename such as *_varna_colors.txt.

These reactivity profiles have the same values as .map profiles, but have been simplified to replace values above 0.85 with 0.85, values below 0 with 0, and missing data with 0.

Reactivities will be shown as a smooth color gradient from white at 0 to red at 0.85. Note that VARNA does not have a concept of missing data or excluded positions, so positions with low read depth or high background reactivity will show up as white, the same as lowly reactive nucleotides.

Ribosketch coloring

Click Load colors and select a file output by ShapeMapper such as *_ribosketch_colors.txt.

These reactivity profiles have the same values as .map profiles, but have been simplified to replace values above 0.85 with 0.85, values below 0 with 0, and missing data with 0.

Reactivities will be shown as a smooth gradient from white at 0 to red at 0.85, with nucleotides missing data shown as white.

RNAstructure Structure Editor coloring

Click Format → Color-Annotate Bases → Chemical Modification → Load File and select a .shape file output by ShapeMapper.

Click any combination of Text, Fill, and Outlines to apply reactivity colors to nucleotides. The reactivity legend is displayed in the Color Annotations dialog in Value Ranges and Colors. By default, missing data is shown in black (the same as lowly reactive positions). To change this, change the numeric limit for Black from "-INF" to "-990", click Add rule, and set the numeric limit for Gray to "-INF".

XRNA coloring

A .shape or .map file can be passed to the pvclient.py script (included with Superfold) using the --shape parameter along with a .ct file to generate a .xrna file with SHAPE reactivity coloring. The pvclient.py script requires an active internet connection and relies on the Pseudoviewer web service.

Reactivities >= 0.85 are colored red, >= 0.4 orange, < 0.4 black, and missing data gray. The generated .xrna file can be loaded into XRNA for manual layout adjustment and rendering.

    

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