SQUARNA

SQUARNA predicts RNA secondary structures, including pseudoknots and alternative conformations, to support analysis of RNA structure-function relationships and comparative studies.

Key Features:

• Input Flexibility: Accepts single RNA sequences and alignments of sequences as input.
• Pseudoknot Handling: Incorporates pseudoknots into secondary-structure predictions.
• Alternative Structures Prediction: Generates multiple alternative secondary-structure models for a given sequence or alignment.
• Structural Restraints and Chemical Probing Integration: Accepts structural restraints and chemical probing data to inform and constrain predictions.
• Prediction Model: Implements a simple, greedy stem formation model for de novo secondary-structure prediction.
• Performance Benchmarking: Benchmarked against leading methods, showing comparable performance for single sequences and superior results on sequence alignments.

Scientific Applications:

• Non-coding RNA Structural Analysis: Supports inference of secondary structure for non-coding RNAs relevant to their cellular functions.
• Structure–Function Inference: Enables investigation of functional implications of secondary structures, including pseudoknots and alternative conformations.
• Comparative and Evolutionary Analysis: Applicable to comparative studies and evolutionary analyses that use sequence alignments to inform structure prediction.

Methodology:

The core method uses a simple greedy stem formation model and operates on single sequences or sequence alignments while allowing incorporation of structural restraints and chemical probing data.