Skipper

Skipper performs enhanced analysis of crosslinking and immunoprecipitation followed by sequencing (CLIP-seq) datasets to identify transcriptomic binding sites of RNA-binding proteins and to characterize determinants of translation factor occupancy.

Key Features:

• Improved statistical framework: Calls transcriptomic binding sites using enhanced statistical approaches for CLIP-seq data.
• Increased sensitivity and specificity: Calls 210%–320% more transcriptomic binding sites on average and over 1,000% more in some datasets compared to existing methods.
• Comprehensive coverage of repetitive elements: Identifies binding sites across annotated repetitive elements and calls bound elements for 99% of enhanced CLIP experiments.
• End-to-end read processing: Converts unprocessed reads into annotated binding sites through a complete workflow.
• Translation factor occupancy analysis: Enables analysis of determinants of translation factor occupancy including transcript region, sequence, and subcellular localization.
• Genetic variation analysis: Detects depletion of genetic variation at sites occupied by translation factors to nominate transcripts under selective constraint.

Scientific Applications:

• Post-transcriptional regulation: Identification of RNA-binding protein binding sites to study mechanisms of post-transcriptional gene regulation.
• RNA–protein interaction mapping: Discovery of novel binding sites across CLIP-seq datasets, including within annotated repetitive elements.
• Translation factor studies: Characterization of factors that determine translation factor occupancy by transcript region, sequence, and subcellular localization.
• Evolutionary and genetic constraint analysis: Nomination of transcripts under selective constraint via depletion of genetic variation at occupied sites.

Methodology:

Converts unprocessed reads into annotated binding sites and applies statistical frameworks to call transcriptomic binding sites and bound elements, including across annotated repetitive elements.