Skip to content

RNAFramework Fold Specifications

Process Details

  • Name: RNAFramework Fold
  • Process UUID: 3d26678c1bab45428d77888e143add76
  • Process Group: Misc.

Overview

This module predicts RNA secondary structure by folding RNA sequences using normalized chemical probing reactivities as constraints, producing experimentally informed structure models. The process integrates experimental chemical probing data with computational folding algorithms to generate more accurate RNA secondary structure predictions.

This process is implemented in Bash, which invokes the RNAFramework rf-fold tool for RNA secondary structure prediction.

Key Functionality

  • Structure Prediction: Predicts RNA secondary structures using chemical probing data as folding constraints
  • Multiple Folding Methods: Supports both ViennaRNA and RNAstructure folding algorithms
  • Pseudoknot Detection: Optional detection of pseudoknot structures using specialized algorithms
  • Output Flexibility: Generates structures in dot-bracket notation or connectivity table format

Input/Output Specification

Inputs

Required Inputs

  • Transcript Reactivity
    • Description: XML file containing normalized chemical probing reactivities for RNA transcripts
    • Format: XML

Outputs

  • Directory
    • Description: Output directory containing predicted RNA secondary structures, images, and dot-plots
    • Format: Directory

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Folding method

    • Description: Specifies the folding method (Default: ViennaRNA)
    • Available options: ViennaRNA (default), RNAstructure

  • Output type

    • Description: Writes predicted structures in Dot-bracket notation or CT format (Default: Dot-bracket notation)
    • Available options: Dot-bracket notation (default), Connectivity table

  • Temperature

    • Description: Temperature in Celsius degrees (Default: 37.0)
    • Default value: 37.0

  • Slope

    • Description: Sets slope used with structural probing data restraints (Default: 1.8 [kcal/mol])
    • Default value: 1.8

  • Intercept

    • Description: Sets intercept used with structural probing data restraints (Default: -0.6 [kcal/mol])
    • Default value: -0.6

  • Activate windowed folding

    • Description: Enables windowed folding for longer transcripts
    • Default value: false

  • Detect pseudoknots

    • Description: Enables detection of pseudoknots (computationally intensive)
    • Default value: true

  • Pseudoknot algorithm

    • Description: Algorithm for pseudoknots prediction (Default: RNA Framework)
    • Available options: RNA Framework (default), ShapeKnots

  • Subopt. delta energy

    • Description: Computes suboptimal structures with energy in a certain range of the optimum (>=0, Default: 1 [kcal/mol])
    • Default value: 1.0

  • Pseudoknot subopt. structures

    • Description: Number of suboptimal structures to evaluate for pseudoknots prediction (>0, Default: 1000)
    • Default value: 1000

  • Disable Zuker suboptimal structures

    • Description: Disables the inclusion of Zuker suboptimal structures (reduces the sampled folding space)
    • Default value: false

  • Number of Zuker subopt. structures

    • Description: Number of Zuker suboptimal structures to include (>0, Default: 1000)
    • Default value: 1000

  • Other Parameters

    • Description: Additional command-line parameters for advanced users including options for constraint files, partition function calculations, and pseudoknot-specific parameters
    • Default value: (empty)

References & Resources

  • Tool Documentation: Contact the team for details on rf-fold