CLIPZ

CLIPZ provides analysis and visualization of short reads from cross-linking and immunoprecipitation (CLIP) deep sequencing to map RNA-binding protein binding sites and annotate post-transcriptional regulatory elements across the transcriptome.

Key Features:

• Visualization and analysis: Genome-wide visualization at genomic and transcript levels for identification and analysis of RNA-binding protein (RBP) binding sites and post-transcriptional regulatory elements.
• Support for CLIP and short-read experiments: Processes short reads from cross-linking and immunoprecipitation (CLIP) experiments and other short-read sequencing datasets.
• RBP coverage: Includes binding site data for Argonaute 1-4, Insulin-like growth factor II mRNA-binding protein 1-3, TNRC6 proteins A-C, Pumilio 2, Quaking, and Polypyrimidine tract binding protein.
• High-throughput data handling: Handles large volumes of deep-sequencing data to enable transcriptome-wide analysis of RNA–protein interactions.
• Functional annotation: Enables functional annotation of RBP binding sites to support downstream biological interpretation.

Scientific Applications:

• RBP binding site mapping: High-resolution mapping of RNA-binding protein binding sites across transcripts from CLIP datasets.
• mRNA regulation studies: Investigation of mRNA stability, localization, and translation regulation mediated by RBPs.
• Transcriptomic analyses: Analysis of short-read sequencing data from non-CLIP experiments for broader transcriptomic studies.
• Regulatory element identification: Identification and annotation of post-transcriptional regulatory elements to inform studies of gene expression control and potential therapeutic targets.

Methodology:

Processes short reads derived from cross-linking and immunoprecipitation (CLIP) coupled with deep sequencing to identify and annotate RNA–protein interaction sites across the transcriptome.