Freiburg RNA Tools

Freiburg RNA Tools provides a suite of computational methods for RNA sequence and structure analysis, RNA–RNA interaction prediction, small RNA homology search, CRISPR repeat classification, sequence design, structure-aberration evaluation, and model visualization for RNA and protein families.

Key Features:

• RNA-RNA Interaction Prediction: Implements IntaRNA, CopraRNA, and metaMIR for predicting interactions between RNA molecules.
• sRNA Homology Search: Uses GLASSgo to identify homologs of small RNAs (sRNAs) across species.
• Sequence-Structure Alignments: Performs sequence-structure-aware alignments using LocARNA, MARNA, CARNA, and ExpaRNA.
• CRISPR Repeat Classification: Provides CRISPRmap for classification and analysis of CRISPR repeats.
• Sequence Design: Includes antaRNA, INFO-RNA, and SECISDesign for designing RNA sequences with specified properties.
• Structure Aberration Evaluation: Offers RaSE to evaluate the effects of point mutations on RNA secondary structure.
• RNA/Protein-Family Models Visualization: Enables CMV to visualize models of RNA and protein families.

Scientific Applications:

• Regulatory interaction analysis: Predicting and analyzing RNA–RNA interactions to infer potential functional relationships and regulatory mechanisms.
• sRNA conservation and discovery: Identifying conserved sRNA homologs across species.
• Structure-function analysis: Assessing functional implications of structural variations via sequence-structure alignments.
• CRISPR system studies: Classifying CRISPR repeats to study diversity and evolution of CRISPR systems.
• Synthetic biology and design: Designing RNA sequences for synthetic biology and functional engineering.
• Mutation impact prediction: Predicting the effects of point mutations on RNA structure and potential function.
• Model interpretation: Visualizing RNA and protein-family models to interpret structural and functional relationships.

Methodology:

Implements algorithms and models embodied in IntaRNA, CopraRNA, metaMIR, GLASSgo, LocARNA, MARNA, CARNA, ExpaRNA, CRISPRmap, antaRNA, INFO-RNA, SECISDesign, RaSE, and CMV.