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vaRRI

This Tool creates a visualization for any working inter- and intramolecular structure and sequence involving one or two molecules, using FornaC.

Example interaction between the molecule MicF and IpxR, displayed in this paper also generated using vaRRI

 
./rna_to_img.py -o=example.svg --startIndex1=67 --sequence="GCCAGUAGCCUUGCUAUUUCAGUGGCGAAUGAUGAUGCAGGU&GCUAUCAUCAUUAACUUUAUUUAU" --structure="...(((((............(((....(((((((((((....&)).))))))))).))))))))..." --accessibility1="RNAplfold" --accessibility2="RNAplfold"

Overview

Installation

We need to install

  • playwright (tested and developed with v1.57.0)
  • chromium browser (install via playwright)
# install dependencies
python3 -m pip install playwright==1.57.0
python3 -m playwright install chromium
# check version
python3 -m playwright --version

Features

Mandatory Parameters

--structure Specifies the RNA secondary structure in dot-bracket notation.
Notation Meaning
( ) Base pair
[ ] Alternative bracket pair
< > Alternative bracket pair
{ } Alternative bracket pair
. Unpaired nucleotide
& Separator between two molecules (intermolecular interaction)
intramolecular: 

rna_to_img.py \
  -u="((...))...." \
  -e="NNNNNNNNNNN"
intermolecular: 

rna_to_img.py \
  -u="((...))..<<..&...>>.." \
  -e="NNNNNNNNNNNNN&NNNNNNN"
Hybrid Input Format (Advanced)

The hybrid input format provides a convenient way to specify intermolecular base pairing interactions using position indices instead of dot-bracket notation.

Format:

<start_pos_1><pipes_and_dots>&<start_pos_2><pipes_and_dots>

Where:

  • <start_pos>: Starting position (index, can be negative, can not be 0)
  • |: Represents a base pair in the intermolecular interaction
  • .: Represents an unpaired position within the interaction region

How it works:

  • Both molecules must have the same number of | characters (representing the same number of base pairs)
  • Interaction positions are defined relative to your sequence start Index
  • The tool automatically converts hybrid input to standard dot-bracket notation
Example (simple interaction):
Two sequences with interaction starting at position 5 (seq1) and position 3 (seq2) and each has 3 intermolecular base pairs 

./rna_to_img.py \
  -u="5|||..&3|||.." \
  -e="NNNNNNNNNNNNN&NNNNNNN"
Example (with custom start Index)
Start indexing from position 10 (seq1) and 100 (seq2)
Interaction starts at position 15 (seq1) and 102 (seq2) 

rna_to_img.py \
  -u="15|||..&102|||.." \
  -e="NNNNNNNNNNNNN&NNNNNNN" \
  -i1=10 \
  -i2=100
Example (negative positions):
start indexing form -10 (seq1) and 1 (seq2)
Interaction starts at position -5 (seq1) and 3 (seq2) 

rna_to_img.py \
  -u="-5|||..&3|||.." \
  -e="NNNNNNNNNNNNN&NNNNNNN" \
  -i1=-10 \
  -i2=1

Hybrid vs. Dot-Bracket Comparison: These two commands are equivalent:

Hybrid format: 

rna_to_img.py \
  -u="5|||..&3|||" \
  -e="NNNNNNNNNNNNNN&NNNNN"
Equivalent dot-bracket format: 

rna_to_img.py \
  -u="....(((......&..))).." \
  -e="NNNNNNNNNNNNN&NNNNNNN"

--sequence Specifies the RNA sequence using IUPAC nucleotide codes (see also --fastafile)
Code Nucleotide Code Nucleotide
A Adenosine N Any nucleotide
C Cytidine W Adenosine or Uridine
G Guanosine S Cytidine or Guanosine
U Uridine K Guanosine or Uridine
& Separator between two molecules
Example: 

rna_to_img.py -u=".((...))." -e="AACGAGUGA"

Optional Parameters

-o/ --output Specifies the output file name and format
Value Description
STDOUT (default) Print SVG to standard output
filename Save as SVG with given name
filename.png Save as PNG with given name

Examples:

# Output to stdout
rna_to_img.py -u="((...))." -e="ACGAGUGA" > output.svg

# Save as SVG file
rna_to_img.py -u="((...))." -e="ACGAGUGA" -o=structure

# Save as PNG file
rna_to_img.py -u="((...))." -e="ACGAGUGA" -o=structure.png
-c/ --coloring Defines how nucleotides should be colored
Option Description Example
loop Standard fornac coloring scheme
strand (default) Each molecule receives its own color
Example: 

rna_to_img.py \
  -u="((...))..<<..&...>>.." \
  -e="NNNNNNNNNNNNN&NNNNNNN" \
  -c=strand
-H/ --highlighting Specifies the highlighting mode for intermolecular structures
Option Example Image
nothing: no sepcial highlighting 

rna_to_img.py \
  -u="((...))..<<....<<..&..>>...>>.." \
  -e="NNNNNNNNNNNNNNNNNNN&NNNNNNNNNNN" \
  -H=nothing \
  -c=loop
basepairs: Highlights only individual intermolecular base pairs 

rna_to_img.py \
  -u="((...))..<<....<<..&..>>...>>.." \
  -e="NNNNNNNNNNNNNNNNNNN&NNNNNNNNNNN" \
  -H=basepairs
region(default): Highlights entire intermolecular interaction region 

rna_to_img.py \
  -u="((...))..<<....<<..&..>>...>>.." \
  -e="NNNNNNNNNNNNNNNNNNN&NNNNNNNNNNN" \
  -H=region
-bH/ --backgroundhighlighting Specifies the background highlighting mode for intermolecular interactions
Option Description
nothing no background highlighting
basepairs (default) highlights intermolecular basepair stacking
region highlights the full intermolecular interaction region 
rna_to_img.py \
  --structure="((...))..<<..&...>>.." \
  --sequence="NNNNNNNNNNNNN&NNNNNNN" \
  -bH=region
-i1/ --startIndex1, -i2/ --startIndex2 Sets the starting index for each molecule
Parameter Constraint
Default 1
Restriction Cannot be 0
Example: Indexing starts with 10 

rna_to_img.py \
  -u="..((...))." \
  -e="AAACGAGUGA" \
  -i1=10
Example: Both molecules have different start indicies 

rna_to_img.py \
  -u="((...))..<<..&...>>.." \
  -e="NNNNNNNNNNNNN&NNNNNNN" \
  -i1=5 \
  -i2=100
-v/ --verbose Enables detailed logging output for debugging and troubleshooting 
./rna_to_img.py -u="((...))." -e="ACGAGUGA" -v
-l/ --labelInterval Defines how often labels with indices are displayed
Option Description
n Shows index labels every n nucleotides
10 default 
rna_to_img.py \
  -u="((...))....((...))" \
  -e="ACGAGUGAACGAGUGA" \
  -l=5
--crop, --crop1, --crop2 Crops sequences around the intermolecular interaction region
Parameter Description
--crop Applies cropping to both molecules
--crop1 Crops only the first molecule
--crop2 Crops only the second molecule 
rna_to_img.py \
  -u="((...))..<<..&...>>.." \
  -e="NNNNNNNNNNNNN&NNNNNNN" \
  --crop=5
--highlightSubseq1, --highlightSubseq2 Highlights specific subsequences
Parameter Description
--highlightSubseq1 Subsequences in first molecule
--highlightSubseq2 Subsequences in second molecule 
rna_to_img.py \
  -u="((...))..<<..&...>>.." \
  -e="NNNNNNNNNNNNN&NNNNNNN" \
  --highlightSubseq1="1:2,5:10"
--guBasepairs Controls visualization of G-U base pairs
Option Description
Enabled (default) G-U basepairs shown as dashed lines
Disabled No special visualization 
rna_to_img.py \
  -u="((...))" \
  -e="GUGUGUGU" \
  --guBasepairs
--fastafile Load one or two sequences from a FASTA file 
rna_to_img.py \
  --fastafile=example.fasta \
  -u="((...))"
--predictStructure1, --predictStructure2 Enable intramolecular structure prediction
Flag Option Description
Enabled Predict intramolecular structure for each molecule. Using RNAfold with constraints: --structure given Basepairs
Disabled (default) No structure prediction 
rna_to_img.py \
  -e="ACGAGUGA" \
  --predictStructure1
--animation Activates fornac’s force-directed layout animation 
rna_to_img.py \
  -u="((...))" \
  -e="ACGAGUGA" \
  --animation
--accessibility1, --accessibility2 Visualize nucleotide accessibility
Option Description
None (default) No visualization
RNAplfold Predict accessibility using RNAplfold
path/to/file Use precomputed lunp file 
rna_to_img.py \
  -u="((...))" \
  -e="ACGAGUGA" \
  --accessibility1="RNAplfold"
--RNAfold Pass custom parameters to RNAfold 
rna_to_img.py \
  -e="ACGAGUGA" \
  --predictStructure1 \
  --RNAfold="-T20"
--RNAplfold Pass custom parameters to RNAplfold 
rna_to_img.py \
  -e="ACGAGUGA" \
  --accessibility1="RNAplfold" \
  --RNAplfold="-T20"

Usage Examples

Simple Intramolecular Structure
Visualization of a single RNA molecule with one hairpin loop: 

rna_to_img.py -u=".((...))." -e="AACGAGUGA" > hairpin.svg
Intermolecular Interaction with Distinct Coloring
Two molecules interacting where each molecule has its own color: 

rna_to_img.py \
  -u="((...))..<<..&...>>.." \
  -e="NNNNNNNNNNNNN&NNNNNNN" \
  -c=strand \
  -o=interaction.svg
Custom Indexing
Start numbering from different positions for each molecule: 

rna_to_img.py \
  -u="((...))..<<..&...>>.." \
  -e="NNNNNNNNNNNNN&NNNNNNN" \
  -i1=5 -i2=100 \
  -o=custom_index.svg
Pseudoknot Structure (Simple)
A basic pseudoknot involving two interacting molecules: 

rna_to_img.py \
  -u="<<<..((..>>>&<<<..))..>>>" \
  -e="NNNNNNNNNNN&NNNNNNNNNNNN" \
  -c=strand \
  -o=pseudoknot_simple.svg
Pseudoknot Structure (Complex - Kissing Hairpins)
Two molecules forming a complex kissing hairpin interaction: 

rna_to_img.py \
  -u="<<<..(((..>>>...<<<..(((..>>>..&<<<..)))..>>>...<<<..)))..>>>.." \
  -e="NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN&NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN" \ 
  -c=strand \ 
  -o=kissing_hairpins.svg