RNAex

RNAex predicts RNA secondary structures by integrating high-throughput structure probing data with thermodynamic folding models across multiple species.

Key Features:

• Probing Data–Guided Folding: Incorporates high-throughput in vivo and in vitro structure probing data into restrained MaxExpect, SeqFold, RNAstructure (Fold), and RNAfold algorithms to improve secondary structure prediction accuracy.
• Genomic Remapping and Structural Annotation: Remaps raw probing sequencing data to whole genomes of human, mouse, yeast, and Arabidopsis and annotates predicted structures with RNA editing sites, RNA modifications, and single nucleotide polymorphisms (SNPs).

Scientific Applications:

• Comparative and Functional RNA Structure Analysis: Enables experimentally informed secondary structure prediction and variant annotation for known and novel transcripts across species.

Methodology:

RNAex combines statistical processing of high-throughput probing datasets with free energy–based folding algorithms to generate experimentally constrained RNA secondary structure models and associated genomic annotations.