rnaCrosslinkOO

rnaCrosslinkOO analyzes RNA structural data from Crosslinking of Matched RNA and Deep Sequencing (COMRADES) experiments, enabling processing, clustering, and comparative analysis of in vivo RNA secondary and tertiary structures.

Key Features:

• COMRADES-Based Analysis Pipeline: Processes raw sequencing reads through alignment, duplex clustering, and folding analysis to identify RNA structural features.
• Inter- and Intra-RNA Interaction Detection: Identifies RNA duplexes, compares structures across conditions, and integrates reactivity data to refine structure interpretation.

Scientific Applications:

• In Vivo RNA Structure and Interaction Studies: Supports investigation of RNA secondary and tertiary structures, RNA–RNA interactions, and condition-dependent structural variation.

Methodology:

rnaCrosslinkOO implements an object-oriented R-based pipeline tailored to COMRADES data, including read alignment, duplex clustering, structural comparison, and integration of experimental reactivity information for RNA folding analysis.