RNApredator

RNApredator predicts bacterial sRNA–mRNA interactions using the RNAplex dynamic programming algorithm with target accessibility modeling across a large genome database.

Key Features:

• RNAplex-Based Interaction Prediction: Applies the RNAplex dynamic programming algorithm to identify potential sRNA–mRNA interactions efficiently across 2155 genomes and plasmids from 1183 bacterial species.
• Target Accessibility and Functional Post-Processing: Incorporates mRNA target accessibility into binding predictions and performs automated post-processing including Gene Ontology enrichment, pathway analysis, and positional accessibility profiling along mRNA sequences.

Scientific Applications:

• Bacterial Post-Transcriptional Regulation Analysis: Supports high-throughput identification of sRNA targets to investigate regulatory networks underlying bacterial physiology and pathogenicity.

Methodology:

RNApredator uses the RNAplex dynamic programming framework to compute sRNA–mRNA hybridization energies while modeling target site accessibility, followed by automated functional enrichment and pathway analyses to interpret predicted regulatory interactions.