Ribosome Stalling - Usage Guide

Ribosome Stalling - Usage Guide

Overview

Detect ribosome pausing and stalling sites at codon resolution to study translational regulation, rare codon effects, and nascent chain interactions.

Prerequisites

pip install plastid numpy scipy biopython

Quick Start

Tell your AI agent:

• "Find ribosome pause sites in my Ribo-seq data"
• "Calculate codon-specific ribosome occupancy"
• "Identify stalling at rare codons"
• "Analyze pause motifs"

Example Prompts

Pause Site Detection

"Find positions with elevated ribosome occupancy (z-score > 3)"

"Identify stalling sites in my genes of interest"

"How many pause sites are there per gene?"

Codon Analysis

"Calculate average ribosome occupancy per codon"

"Which codons have highest pause frequency?"

"Correlate pausing with tRNA abundance"

Motif Analysis

"What amino acid motifs are enriched at pause sites?"

"Find polyproline-associated stalling"

"Analyze context around pause sites"

What the Agent Will Do

1. Map reads to P-site positions using offset
2. Calculate codon-level ribosome occupancy
3. Identify positions with elevated occupancy (z-score)
4. Aggregate by codon type
5. Analyze sequence/motif context

Tips

• Correct P-site offset is critical for codon assignment
• Z-score > 3 is a typical threshold for pause sites
• Normalize by gene expression to compare across genes
• Polyproline (PPP) is a well-known pause motif
• Rare codons correlate with pausing (tRNA limitation)