CTK

CTK analyzes data from UV cross-linking and immunoprecipitation (CLIP) experiments followed by high-throughput sequencing to map protein–RNA interactions genome-wide in vivo.

Key Features:

• CLIP data analysis: Analyzes data derived from UV cross-linking and immunoprecipitation (CLIP) followed by high-throughput sequencing to identify protein–RNA interaction sites.
• CIMS integration: Builds upon the CIMS package and extends its functionality for CLIP-specific analyses.
• Implementation: Implemented in Perl.
• Scalability: Handles large-scale high-throughput sequencing datasets efficiently.
• Analytical workflows: Provides workflows that support a range of analytical tasks for interpreting complex CLIP sequencing datasets.
• Genome-wide mapping: Enables genome-wide, in vivo mapping of RNA-binding protein (RBP) interactions.

Scientific Applications:

• RBP binding-site mapping: Mapping RNA-binding protein (RBP) binding sites genome-wide in vivo.
• Post-transcriptional regulation: Investigating RBP roles in post-transcriptional regulation, including splicing, RNA stability, and localization.
• Functional genomics: Supporting functional genomics studies of gene expression regulation through protein–RNA interaction data.

Methodology:

Implemented in Perl and built upon the CIMS package to analyze high-throughput sequencing data from UV cross-linking and immunoprecipitation (CLIP) experiments and to provide downstream analytical workflows.