CapR

CapR computes per-base probabilities that nucleotides in RNA sequences occupy specific secondary structural contexts to characterize structural environments relevant to RNA-binding protein (RBP) interactions and to analyze high-throughput CLIP-seq data.

Key Features:

• Probability calculation: CapR computes the probability that each base position within long RNA sequences resides in defined secondary structural contexts.
• Structural context analysis: CapR characterizes conformational preferences of RNA secondary structures relevant to RBP binding.
• High-throughput CLIP-seq data analysis: CapR processes CLIP-seq and related high-throughput sequencing data to annotate RBP-bound RNA fragments with structural-context probabilities.
• Computational efficiency: CapR implements an algorithmic approach optimized for large datasets typical of CLIP-seq experiments.

Scientific Applications:

• RBP-RNA interaction studies: Identification and characterization of structural contexts preferred by specific RBPs.
• Functional genomics: Investigation of how RNA secondary structure influences RBP-mediated regulation of gene expression.
• Structural biology and molecular dynamics: Integration of sequence-based interaction data with RNA secondary-structure context to inform structural interpretations of RBP binding.

Methodology:

CapR uses CLIP-seq and related high-throughput sequencing data to map RBP-RNA interactions and applies an algorithmic probabilistic approach to assess the likelihood that each RNA base is part of specific secondary-structure contexts.