Agent skill

Bio Ribo Seq Initiation Site Mapping

by GPTomics in GPTomics/bioSkills

Map translation initiation sites, including non-AUG and alternative starts, from initiation-drug ribosome profiling (TI-seq).

MITAuto-check passedWriting & Content

Install Bio Ribo Seq Initiation Site Mapping

skills CLI
$ npx skills add GPTomics/bioSkills --skill bio-ribo-seq-initiation-site-mapping -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install GPTomics/bioSkills bio-ribo-seq-initiation-site-mapping --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/GPTomics/bioSkills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/ribo-seq/initiation-site-mapping .claude/skills/bio-ribo-seq-initiation-site-mapping && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
bio-ribo-seq-initiation-site-mapping
GitHub stars
1.2k
Used in
1 other repo
Token cost
~2k tokens
SKILL.md length
899 words
Files
3
Skills in repo
559
Repo updated
First seen
Licence
MIT

At a glance

Map translation initiation sites, including non-AUG and alternative starts, from initiation-drug ribosome profiling (TI-seq).

  • Locating start codons
  • SKILL.md covers Version Compatibility, Initiation-drug data types…, Near-cognate and alternative… and Tool selection, plus 7 more sections
  • Runs Shell scripts from its folder; calls pip
  • Detecting near-cognate

What it does

Bio Ribo Seq Initiation Site Mapping is an agent skill from GPTomics/bioSkills. Map translation initiation sites, including non-AUG and alternative starts, from initiation-drug ribosome profiling (TI-seq). Use when locating start codons, detecting near-cognate or upstream initiation, or analyzing harringtonine, lactimidomycin (GTI-seq/QTI-seq), or retapamulin (Ribo-RET) data.

Its SKILL.md is about 2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/map_initiation_sites.sh` and `usage-guide.md`).

It sits in Writing & Content, covering Translation. The repository describes itself as: a set of SKILLS.md for doing bioinformatics with agents like claude code. The licence is MIT.

When your agent uses it

  • Locating start codons
  • Detecting near-cognate
  • Upstream initiation
  • Analyzing harringtonine

Example prompts

  • “/bio-ribo-seq-initiation-site-mapping”

Requirements

  • A Bash shell

What it can do on your machine

Read from SKILL.md and the folder at commit d91ed3d. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships script files (Shell), which the agent can run.

    Shell commands in SKILL.md call:

    • pip

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Bio Ribo Seq Initiation Site Mapping loads about 2k tokens when it runs. Until then it costs about 84 tokens; SKILL.md has 899 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~84
When it runs · the whole SKILL.md, loaded when a task matches
~2k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from GPTomics/bioSkills at commit d91ed3d, republished under its MIT licence (© GPTomics). 899 words, ~1,999 tokens.

Download SKILL.mdSave it as .claude/skills/bio-ribo-seq-initiation-site-mapping/SKILL.md (or your agent's skills folder). This skill also uses 2 other files; get the full folder from GitHub.
name
bio-ribo-seq-initiation-site-mapping
description
Map translation initiation sites, including non-AUG and alternative starts, from initiation-drug ribosome profiling (TI-seq). Use when locating start codons, detecting near-cognate or upstream initiation, or analyzing harringtonine, lactimidomycin (GTI-seq/QTI-seq), or retapamulin (Ribo-RET) data.
tool_type
mixed
primary_tool
Ribo-TISH

Version Compatibility

Reference examples tested with: Ribo-TISH 0.2.7+, PRICE/GEDI 1.0.5+, samtools 1.19+

Before using code patterns, verify installed versions match. If versions differ:

  • CLI: <tool> --version then <tool> --help to confirm flags
  • Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Translation Initiation Site Mapping

"Map where translation starts in my Ribo-seq data" -> Locate translation initiation sites (TIS) at single-nucleotide resolution, including non-AUG and upstream starts, from initiation-drug profiling experiments.

  • CLI: Ribo-TISH for TIS detection from harringtonine/LTM data; PRICE for EM-based cryptic-start detection

This is a distinct analysis from elongation ORF detection: it asks WHERE initiation occurs (which start codon), not which ORF bodies are translated. It typically requires a dedicated initiation-drug library paired with a standard elongation library.

Initiation-drug data types (which experiment produced the data)

MethodDrug(s)SignalCitation
Harringtonine TISharringtoninebinds free 60S, blocks the first peptide bond; broad start peakIngolia 2011
GTI-seqlactimidomycin (LTM) + CHX in parallelLTM blocks translocation at the assembled 80S; sharp start peakLee 2012
QTI-seqLTM then puromycin (sequential)puromycin strips elongating ribosomes; quantitative, low backgroundGao 2015
Ribo-RET (bacteria)retapamulinarrests initiating 70S at start codonsMeydan 2019

All three drugs CREATE the initiation signal by halting or removing elongation; the data is a deliberate artifact read out at the start codon. LTM gives sharper peaks than harringtonine because it cannot act on elongating ribosomes whose E-site is occupied. QTI-seq (LTM then puromycin) is analyzed on the same LTM path below; the puromycin step only strips elongating ribosomes to lower the background, so the TIS library is still passed as the LTM-type -t input. Without an initiation-drug library, start codons can only be inferred indirectly from elongation periodicity (see orf-detection).

Near-cognate and alternative starts

Initiation occurs at AUG and near-cognate codons differing by one base; the biologically used set is CUG, GUG, ACG, UUG, AUU, AUC, AUA (AAG/AGG also differ by one base but initiate negligibly). CUG is the dominant near-cognate start (~16% of mapped sites in GTI-seq; AUG remains >50%). uORFs especially use near-cognate starts, so initiation mapping must enable alternative start codons to recover them; an AUG-only search misses most upstream initiation.

Tool selection

SituationToolWhy
TIS from harringtonine/LTM data, with QCRibo-TISHquality + predict modes; near-cognate via --alt; differential TIS
Cryptic/near-cognate starts, EM modelPRICEper-codon EM; handles near-cognate; designed for cryptic events
Bacterial initiation (Ribo-RET)dedicated retapamulin analysisprokaryote initiation; eukaryote periodicity tools fit poorly

QC the initiation library

Goal: Confirm the drug enriched start-codon signal and pick P-site offsets before predicting.

Approach: Run Ribo-TISH quality, which reports the metagene profile and writes a per-length offset parameter file.

bash
# Writes a <ribo.bam>.para.py offset file and a QC figure
ribotish quality -b ribo_elongation.bam -g annotation.gtf -o ribo_quality.txt -f ribo_qc.pdf
ribotish quality -b ribo_tis.bam -g annotation.gtf -o tis_quality.txt -f tis_qc.pdf

Predict initiation sites with Ribo-TISH

Goal: Call TIS, including non-AUG starts, using the initiation-drug library.

Approach: Run ribotish predict with the elongation BAM (-b) and the TIS/harringtonine/LTM BAM (-t), enabling alternative start codons.

bash
# --harr marks the TIS library as harringtonine-type; --alt enables near-cognate starts
ribotish predict \
    -b ribo_elongation.bam \
    -t ribo_tis.bam \
    -g annotation.gtf \
    -f genome.fa \
    --harr --harrwidth 15 --alt \
    -o tis_predictions.txt

The output lists initiation sites with the start codon, ORF type, and significance. For differential initiation across conditions, ribotish tisdiff compares two TIS libraries.

Show full SKILL.md (384 more words)Show less

Alternative: cryptic starts with PRICE

Goal: Detect cryptic and near-cognate initiation with an EM model.

Approach: Prepare the genome and run the Price tool in GEDI on the Ribo-seq reads.

bash
gedi -e Price -reads ribo_elongation.bam -genomic prepared_genome -prefix price_out

PRICE reports a per-ORF p-value from a generalized binomial model (not multiple-testing corrected); codon-level activity is written to price_out.codons.cit.

Interpreting initiation sites

A called TIS is strongest when it shows a sharp drug-induced start peak, a downstream in-frame elongation signal in the standard library, and (for novel sites) conservation or peptide support. Alternative N-terminal starts and uORF starts frequently use near-cognate codons; report the start codon identity, not just the position. Initiation at a uORF does not guarantee a stable protein product (see orf-detection validation).

Common Errors

SymptomCauseFix
Only AUG starts foundAlternative starts not enabledAdd --alt (Ribo-TISH) or use PRICE for near-cognate
Broad, smeared start peaksHarringtonine data treated as sharp LTM dataUse --harr; expect broader peaks than LTM
predict gives weak callsMissing the paired elongation BAM (-b)Provide both -b (elongation) and -t (TIS) libraries
TIS analysis on elongation-only dataNo initiation-drug library presentInitiation mapping needs harringtonine/LTM/RET data; otherwise infer from periodicity
Bacterial data mis-calledEukaryote TIS tool on Ribo-RET dataUse a retapamulin/prokaryote initiation workflow
  • orf-detection - Call and validate the ORF bodies downstream of mapped starts
  • ribosome-periodicity - Calibrate P-site offsets for both libraries
  • riboseq-preprocessing - Align the elongation and initiation-drug libraries
  • ribosome-stalling - Initiation drugs are not for elongation pausing

References

  • Ingolia NT, Lareau LF, Weissman JS. 2011. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147(4):789-802. doi:10.1016/j.cell.2011.10.002
  • Lee S, Liu B, Lee S, Huang SX, Shen B, Qian SB. 2012. Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. Proc Natl Acad Sci USA 109(37):E2424-E2432. doi:10.1073/pnas.1207846109
  • Gao X, Wan J, Liu B, Ma M, Shen B, Qian SB. 2015. Quantitative profiling of initiating ribosomes in vivo. Nat Methods 12(2):147-153. doi:10.1038/nmeth.3208
  • Zhang P, He D, Xu Y, et al. 2017. Genome-wide identification and differential analysis of translational initiation. Nat Commun 8:1749. doi:10.1038/s41467-017-01981-8
  • Erhard F, Halenius A, Zimmermann C, et al. 2018. Improved Ribo-seq enables identification of cryptic translation events. Nat Methods 15(5):363-366. doi:10.1038/nmeth.4631
  • Meydan S, Marks J, Klepacki D, et al. 2019. Retapamulin-assisted ribosome profiling reveals the alternative bacterial proteome. Mol Cell 74(3):481-493. doi:10.1016/j.molcel.2019.02.017

© GPTomics, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 2 other files in ribo-seq/initiation-site-mapping of GPTomics/bioSkills.

  • SKILL.md
  • examples/map_initiation_sites.sh
  • usage-guide.md

Open the folder on GitHubat commit d91ed3d

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in GPTomics/bioSkills, which our catalogue first saw on October 7, 2026.

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Questions about Bio Ribo Seq Initiation Site Mapping

What does Bio Ribo Seq Initiation Site Mapping do?

Map translation initiation sites, including non-AUG and alternative starts, from initiation-drug ribosome profiling (TI-seq). Bio Ribo Seq Initiation Site Mapping is an agent skill from GPTomics/bioSkills. Map translation initiation sites, including non-AUG and alternative starts, from initiation-drug ribosome profiling (TI-seq).

When should I use Bio Ribo Seq Initiation Site Mapping?

Bio Ribo Seq Initiation Site Mapping fits situations like: locating start codons; detecting near-cognate; upstream initiation; analyzing harringtonine.

How do I install Bio Ribo Seq Initiation Site Mapping in Claude Code?

Run `npx skills add GPTomics/bioSkills --skill bio-ribo-seq-initiation-site-mapping -a claude-code`. Or copy the skill folder (ribo-seq/initiation-site-mapping in GPTomics/bioSkills) into .claude/skills/bio-ribo-seq-initiation-site-mapping in your project. Claude Code loads it when a task matches its description.

How do I install Bio Ribo Seq Initiation Site Mapping in Codex?

Run `npx skills add GPTomics/bioSkills --skill bio-ribo-seq-initiation-site-mapping -a codex`. Or copy the skill folder (ribo-seq/initiation-site-mapping in GPTomics/bioSkills) into .agents/skills/bio-ribo-seq-initiation-site-mapping in your project. Codex loads it when a task matches its description.

Can I use Bio Ribo Seq Initiation Site Mapping in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add GPTomics/bioSkills --skill bio-ribo-seq-initiation-site-mapping -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bio-ribo-seq-initiation-site-mapping, .gemini/skills/bio-ribo-seq-initiation-site-mapping, .github/skills/bio-ribo-seq-initiation-site-mapping and .opencode/skills/bio-ribo-seq-initiation-site-mapping in your project.

What does Bio Ribo Seq Initiation Site Mapping need to run?

Going by SKILL.md and its folder, Bio Ribo Seq Initiation Site Mapping needs a shell for the scripts in its folder and the command-line tools its instructions call (pip). Our summary lists: A Bash shell.

Does Bio Ribo Seq Initiation Site Mapping access the network?

SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.

Is Bio Ribo Seq Initiation Site Mapping safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Bio Ribo Seq Initiation Site Mapping use?

Bio Ribo Seq Initiation Site Mapping is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Bio Ribo Seq Initiation Site Mapping use?

About 2k tokens (SKILL.md is roughly 8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Bio Ribo Seq Initiation Site Mapping?

Skills that share tags, products or a category with Bio Ribo Seq Initiation Site Mapping: Translation Diff Export (Devolutions/UniGetUI, 26k stars), Sync Translations (symfony/symfony, 31k stars), Translation Diff Import (Devolutions/UniGetUI, 26k stars) and Translation Diff Translate (Devolutions/UniGetUI, 26k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Bio Ribo Seq Initiation Site Mapping?

GPTomics (a GitHub organization) maintains it in GPTomics/bioSkills, which has 1,217 GitHub stars. The repository holds 559 skills in this directory. The repository was last updated on August 15, 2026.

Source: GPTomics/bioSkills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.