RNAfdl

RNAfdl visualizes RNA secondary structures and produces intersection-free layouts for representation and analysis of large RNAs (up to 10^3 bases), including ribosome-sized molecules.

Key Features:

• Intersection-Free Diagrams: Produces intersection-free diagrams of RNA secondary structures to represent complex non-crossing base-pairing layouts.
• Large-Scale Structure Capacity: Handles RNA secondary structures of up to 10^3 bases without intersections.
• Output Formats: Exports visualizations in common output formats for downstream use.
• Visualization Styles: Supports classical secondary structure plots, circle plots, linear plots, and mountain plots.
• Automated Minimization: Uses a fully automated conjugate gradients minimization algorithm to optimize drawing of complex structures.
• Implementation: Implemented in C and uses the Cairo 2D graphics library.
• Open Source License: Distributed under the GNU General Public License v3.0.

Scientific Applications:

• Structural biology visualization: Visualizing and interpreting large RNA architectures in structural biology studies.
• Ribosomal and large RNA analysis: Analyzing secondary structure organization in ribosome-sized RNAs and other large noncoding RNAs.
• Secondary-structure exploration: Exploring complex secondary-structure features to inform hypotheses about RNA interactions and functions.

Methodology:

Combines manual editing with an automated conjugate gradients minimization algorithm to generate and refine RNA secondary-structure layouts; implemented in C using the Cairo 2D graphics library.