The RF Fold module is designed to allow transcriptome-wide reconstruction of RNA structures, starting from XML files generated using the RF Norm tool. This tool can process a single, or an entire directory of XML files, and produces the inferred secondary structures (either in dot-bracket notation, or CT format) and their graphical representation (either in Postscript, or SVG format).
Folding inference can be performed using 2 different algorithms:

1. ViennaRNA
2. RNAstructure

Usage

To list the required parameters, simply type:

$ rf-fold -h
Parameter Type Description
-o or --output-dir string Output directory for writing inferred structures (Default: structurome/)
-ow or --overwrite Overwrites the output directory if already exists
-t or --tmp-dir string Path to a directory for temporary files creation (Default: /tmp)
Note: If the provided directory does not exist, it will be created
-ct or --connectivity-table Writes predicted structures in CT format (Default: Dot-bracket notation)
-m or --folding-method int Folding method (1-2, Default: 1):
1. ViennaRNA
2. RNAstructure
-p or --processors int Number of processors (threads) to use (Default: 1)
-g or --img Enables generation of structure representations (Default: Postscript format)
-s or --svg Structure representations are generated in SVG format (requires -g)
-t or --temperature float Temperature in Celsius degrees (Default: 37.0)
-sl or --slope float Sets the slope used with structure probing data restraints (Default: 1.8 [kcal/mol])
-in or --intercept float Sets the intercept used with structure probing data restraints (Default: -0.6 [kcal/mol])
-md or --maximum-distance int Maximum pairing distance (in nt) between transcript's residues (Default: 0 [no limit])
-i or --ignore-reactivity Do not use rf-norm reactivity data to guide folding (MFE unconstrained prediction)
Folding method #1 options (ViennaRNA)
-v or --viennarna string Path to ViennaRNA RNAfold executable (Default: assumes RNAfold is in PATH)
-nlp or --no-lonely-pairs Disallows lonely base-pairs
-ngu or --no-closing-gu Disallows G:U wobbles at the end of helices
-cm or --constraint-method int Method for converting rf-norm reactivities into pseudo-energies (1-2, Default: 1):
1. Deigan et al., 2009
2. Zarringhalam et al., 2012
Zarringhalam et al., 2012 method options
-cc or --constraint-conversion int Method for converting rf-norm reactivities into pairing probabilities (1-5, Default: 1):
1. Skip normalization step (reactivities are treated as pairing probabilities)
2. Linear mapping according to Zarringhalam et al., 2012
3. Use a cutoff to divide nucleotides into paired, and unpaired
4. Linear model for converting reactivities into probabilities of being unpaired
5. Linear model for converting the logarithm of reactivities into probabilities of being unpaired
-bf or --beta-factor float Sets the magnitude of penalities for deviations from the observed pairing probabilities (Default: 0.5)
-f or --cutoff float Cutoff for constraining a position as unpaired (>0, Default: 0.7; requires -cc 3)
-ms or --model-slope float Sets the slope used by the linear model (Default: 0.68 [Method #4], or 1.6 [Method #5]; requires -cc 4 or -cc 5)
-mi or --model-intercept float Sets the intercept used by the linear model (Default: 0.2 [Method #4], or -2.29 [Method #5]; requires -cc 4 or -cc 5)
Folding method #2 options (RNAstructure)
-r or --rnastructure string Path to RNAstructure Fold executable (Default: assumes Fold is in PATH)
-dp or --data-path string Path to RNAstructure data tables (Default: assumes DATAPATH environment variable is already set)

Information

For additional details relatively to ViennaRNA soft-constraint prediction methods, please refer to the ViennaRNA documentation, or to Lorenz et al., 2016 (PMID: 26353838).