RiboCAT

RiboCAT processes capillary electrophoresis nucleic-acid probing data to calculate residue-specific nucleotide reactivities for RNA secondary-structure and RNA-protein interaction analysis.

Key Features:

• Inter-capillary signal alignment: Employs internal size standards for precise alignment of signals across capillaries.
• Peak-sharpening algorithm: Applies a peak-sharpening algorithm to enhance peak identification in electropherograms.
• Residue-specific reactivity calculation: Computes nucleotide/residue-specific reactivities from capillary electrophoresis data.
• Support for chemical and enzymatic probing data including SHAPE: Processes data from chemical and enzymatic probing experiments such as SHAPE.
• Reduced manual intervention and improved reproducibility: Analytical design minimizes manual adjustments to enhance reproducibility of results.

Scientific Applications:

• RNA secondary-structure determination: Uses residue-specific reactivities to inform and validate RNA secondary-structure models.
• RNA-protein interaction analysis: Enables detection of structural changes and protections indicative of RNA-protein interactions.
• SHAPE analysis and validation: Applicable to SHAPE experiments, including studies such as the HIV-1 5' untranslated region (5'UTR) analysis.
• Chemical and enzymatic probing experiments: Facilitates analysis of diverse probing datasets to characterize structured RNAs.

Methodology:

Performs inter-capillary alignment using internal size standards, applies a peak-sharpening algorithm for peak detection, and integrates capillary electrophoresis data with computational algorithms to calculate residue-specific reactivities.