catRAPID omics v2.0

catRAPID omics v2.0 predicts protein-RNA interaction propensities across multiple model organisms to characterize and classify RNA–protein interactions at transcriptome and RNA-binding proteome levels.

Key Features:

• Broad Organism Coverage: Supports eight model organisms for cross-species analysis of protein-RNA interactions.
• Custom Interaction Predictions: Accepts multiple protein and RNA sequences and computes interaction scores between custom sets using updated precompiled libraries.
• Interaction Scoring (catRAPID): Calculates catRAPID scores from sequence data to quantify interaction propensities.
• Enhanced Database Integration: Integrates a newly generated database of RNA-binding motifs to identify motifs within predicted RNA targets.
• Sequence Fragmentation Scheme: Applies sequence fragmentation to handle long linear RNAs and analyze circular RNAs.
• Conservation Analysis: Reports predicted binding sites within protein and RNA sequences for top-scoring pairs and indicates conservation in orthologous protein-RNA pairs.

Scientific Applications:

• Interaction Characterization and Classification: Characterizes and classifies RNA–protein interactions across transcriptomes and RNA-binding proteomes.
• Post-transcriptional Regulation Studies: Supports investigation of mechanisms involved in gene regulation, RNA splicing, and translation control.
• Motif and Binding-site Analysis: Enables identification of RNA-binding motifs within predicted targets and mapping of predicted binding sites on proteins and RNAs.

Methodology:

Computationally calculates catRAPID scores from sequence data using updated precompiled libraries and an integrated RNA-binding motif database, applies sequence fragmentation for long and circular RNAs, identifies predicted binding sites in proteins and RNAs, and assesses conservation in orthologous protein-RNA pairs.