Ribosome Stalling - Usage Guide

Overview

Detect ribosome pausing and stalling at codon resolution to study elongation dynamics, codon dwell times, pause motifs, and ribosome collisions. The decisive judgment is whether a pause is real biology or a cycloheximide artifact, followed by using local-relative occupancy metrics at the A-site rather than a global z-score.

Prerequisites

pip install plastid numpy scipy biopython twobitreader

Quick Start

Tell your AI agent what you want to do: - "Find ribosome pause sites with a local pause score" - "Calculate A-site codon occupancy" - "Check whether my pauses are real or a cycloheximide artifact" - "Look for polyproline and poly-basic stalling"

Example Prompts

Pause Detection

"Score pauses as occupancy over the gene mean, not a global z-score"

"Was my library cycloheximide-treated? Can I trust the dwell times?"

"Which pauses also show up as disome peaks?"

Codon Analysis

"Calculate A-site codon occupancy across the transcriptome"

"How strong is the correlation between codon occupancy and tRNA abundance?"

"Normalize each gene to its own mean before pooling codons"

Motif Analysis

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

"Find polyproline-associated stalling"

"Extract the A-site-centered context around pauses"

What the Agent Will Do

1. Confirm the harvest protocol (drug, freezing) before any dwell claim
2. Map footprints to the calibrated A-site offset
3. Compute per-codon occupancy and local-relative pause scores
4. Require an adequate per-gene coverage floor
5. Extract motif context and cross-check disome/collision evidence

Tips

• Cycloheximide flips conclusions - dwell times are only valid on flash-frozen no-drug data
• A-site for decoding - tRNA/codon effects register at the A-site (P-site + 3)
• Local-relative metrics - pause score = occupancy / gene mean, not a global z-score
• Normalize per gene first - then pool codons (mean-of-ratios)
• Coverage floor - need a few hundred in-frame footprints per gene, not 100
• Disomes confirm pauses - a collision peak coinciding with a monosome pause is strong evidence

Related Skills

• ribosome-periodicity - Calibrate the A-site offset
• orf-detection - Locate ORFs containing pause sites
• initiation-site-mapping - Separate initiation drugs from elongation pausing
• translation-efficiency - Gene-level translation context