Translation Initiation Site Mapping - Usage Guide

Overview

Map translation initiation sites (TIS) at single-nucleotide resolution from initiation-drug ribosome profiling (TI-seq), including non-AUG and alternative starts. This is a distinct analysis from elongation ORF detection: it asks which start codon is used, and it requires a dedicated harringtonine, lactimidomycin (GTI-seq/QTI-seq), or retapamulin (Ribo-RET) library.

Prerequisites

pip install ribotish
# PRICE is distributed as GEDI (Java)

Quick Start

Tell your AI agent what you want to do: - "Map translation initiation sites from my harringtonine Ribo-seq" - "Find non-AUG and uORF start codons with Ribo-TISH" - "Detect cryptic initiation with PRICE" - "Compare initiation between two conditions"

Example Prompts

Initiation Detection

"Run Ribo-TISH predict on my LTM and elongation libraries"

"Enable near-cognate (CUG/GUG) start codons in the search"

"Which uORFs initiate at non-AUG starts?"

Experiment-Specific

"My data is harringtonine - set the harr flag and width"

"Detect cryptic translation events with PRICE"

"I have Ribo-RET bacterial data - how do I map initiation?"

Differential

"Compare initiation-site usage between treatment and control with tisdiff"

"Which start codons change under stress?"

What the Agent Will Do

1. QC each library with ribotish quality and write per-length offsets
2. Run ribotish predict with the elongation and initiation-drug BAMs
3. Enable alternative start codons for near-cognate detection
4. Report initiation sites with start-codon identity and ORF type
5. Optionally compare initiation across conditions

Tips

• Initiation drugs differ - LTM gives sharper peaks than harringtonine
• Pair the libraries - predict needs both elongation (-b) and TIS (-t) BAMs
• Enable alternative starts - uORFs often initiate at CUG/GUG; --alt recovers them
• Report the start codon - alternative N-terminal and uORF starts are often non-AUG
• Bacteria use Ribo-RET - retapamulin, not harringtonine/LTM
• Initiation is not stable protein - a mapped uORF start needs downstream validation

Related Skills

• orf-detection - Call and validate ORF bodies downstream of starts
• ribosome-periodicity - Calibrate P-site offsets
• riboseq-preprocessing - Align both libraries
• ribosome-stalling - Initiation drugs are not for elongation pausing