Peakhood

Peakhood assigns context to CLIP-seq (Crosslinking Immunoprecipitation Sequencing) peaks by determining whether each RNA-binding protein (RBP) binding site maps to a transcript or a genomic region.

Key Features:

• Contextual Assignment: Processes CLIP-seq peak regions produced by conventional peak callers and assigns each peak to a transcript or genomic context by integrating CLIP-seq read data with genomic annotations.
• Splice Variant Identification: For peaks assigned to transcripts, identifies the most likely splice variant associated with each RBP binding site.
• Comprehensive Dataset Merging: Merges results from multiple datasets to produce a consolidated set of transcript-context binding sites across experiments.

Scientific Applications:

• RBP interaction mapping: Refines localization of RNA-binding protein (RBP) binding sites to support studies of RBP–RNA interactions.
• Post-transcriptional regulation analysis: Provides context-specific binding information to inform interpretation of post-transcriptional regulatory mechanisms.
• Alternative splicing studies: Enables identification of splice variants bound by RBPs to support analyses of alternative splicing and its regulatory implications.

Methodology:

Uses peak regions from existing peak callers and integrates CLIP-seq read data with genomic annotations to assign each peak to transcript or genomic context, and performs additional analysis on transcript-assigned peaks to identify the most likely splice variant.