RNAfamProb Plus NeoFold

RNAfamProb Plus NeoFold estimates posterior probabilities for RNA structural alignment to improve comparative analysis of functional non-coding RNAs (ncRNAs). It computes pseudo-probabilities that enhance secondary structure prediction, sequence alignment, consensus secondary structure inference, and structural alignment accuracy.

Key Features:

• Posterior Probability Computation: Calculates pseudo-posterior probabilities for RNA structural alignments to support maximum-expected-accuracy secondary structure estimation.
• Homologous Sequence Integration: Incorporates homologous RNA sequences to leverage evolutionary information for improved structural and alignment predictions.
• Maximum-Expected-Accuracy Optimization: Applies probabilistic scoring to jointly refine sequence alignment and secondary structure prediction.
• Comparative Performance: Demonstrates improved accuracy over state-of-the-art maximum-expected-accuracy secondary structure prediction programs.

Scientific Applications:

• Comparative ncRNA Structural Analysis: Supports accurate structural alignment and evolutionary analysis of RNA families.

Methodology:

RNAfamProb Plus NeoFold computes pseudo-posterior probabilities for structural alignment by jointly modeling RNA sequence alignment and secondary structure formation, integrating homologous sequence information to optimize maximum-expected-accuracy predictions.