PROBer

PROBer quantifies isoform-specific chemical modification profiles from sequencing-based "toeprinting" assays by modeling transcriptase drop-off events to estimate transcript abundances and map RNA structural and modification signals.

Key Features:

• Unified Analysis Platform: Applies a statistical model to resolve isoform-specific modification profiles and estimate transcript abundances from sequencing data in the presence of read multi-mapping.
• Versatility Across Assays: Supports diverse sequencing-based "toeprinting" assays and a range of epitranscriptomic marks within a unified computational framework.
• Performance Superiority: Outperforms assay-specific methods on simulated and biological datasets for accurate modification profiling and abundance estimation.

Scientific Applications:

• RNA Structure: Infers RNA structural elements from chemical modification signatures derived from toeprinting assays.
• RNA Modifications: Detects and profiles chemical RNA modifications across isoforms from sequencing data.
• RNA-Protein Interactions: Maps RNA-protein interaction signals inferred via toeprinting-associated transcriptase drop-off patterns.

Methodology:

Takes raw sequencing data as input and applies a statistical model to estimate transcript abundances and isoform-specific chemical modification profiles while addressing read multi-mapping.