genomics-to-structure-triage

genomics-to-structure-triage is a skill for Claude Code, Codex from Pavel-Kravchenko/Bioinformatics. It costs 63 tokens per session (1,849 once invoked), scanned A, original, no licence file.

A workflow for deciding which protein-structure prediction model to use for coding variants and for ranking the resulting evidence. It combines variant type, expression, rarity, and structure-confidence measures such as pLDDT and PAE.

In plain words
What is it for?
Use it to route variants to AlphaFold2, AlphaFold3, or RoseTTAFold, then prioritize them using missense effects, expression, rarity, and predicted-structure confidence.
Why use it?
It helps narrow a large list of variants to those worth investigating structurally. It also makes model choice and evidence weighting more consistent.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

Good fit Use it to route variants to AlphaFold2, AlphaFold3, or RoseTTAFold, then prioritize them using missense effects, expression, rarity, and predicted-structure confidence.

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Install with agentmods
npx agentmods add skills/pavel-kravchenko/bioinformatics/genomics-to-structure-triage
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add Pavel-Kravchenko/Bioinformatics --skill genomics-to-structure-triage
Clone the repo
git clone --depth 1 https://github.com/Pavel-Kravchenko/Bioinformatics

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for genomics-to-structure-triage

README.md
[![agentmods](https://agentmods.dev/badge/skills/pavel-kravchenko/bioinformatics/genomics-to-structure-triage/github.svg)](https://agentmods.dev/skills/pavel-kravchenko/bioinformatics/genomics-to-structure-triage)
Your own site
<a href="https://agentmods.dev/skills/pavel-kravchenko/bioinformatics/genomics-to-structure-triage"><img src="https://agentmods.dev/badge/skills/pavel-kravchenko/bioinformatics/genomics-to-structure-triage/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for genomics-to-structure-triage

Your own site · 80×15
<a href="https://agentmods.dev/skills/pavel-kravchenko/bioinformatics/genomics-to-structure-triage"><img src="https://agentmods.dev/badge/skills/pavel-kravchenko/bioinformatics/genomics-to-structure-triage.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 63 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,849 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00063 $0.01849
Opus 5 $0.00032 $0.00924
Sonnet 5 $0.00013 $0.00370
Haiku 4.5 $0.00006 $0.00185

Measured 9d ago against content hash e8593fc379e2, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

genomics-to-structure-triage scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

Skills/genomics-to-structure-triage/SKILL.md · 137 lines

The source is not reproduced here

No licence file

A repository with no LICENSE is all rights reserved by default, so the body is not copied here. The metadata, the measurements and the link are.

Read it on GitHub

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 9d ago First seen · 137 lines · 63 tokens per session scan A e8593fc379e2

Subscribe to this mod's changes

genomics-to-structure-triage is a skill published in the GitHub repository Pavel-Kravchenko/Bioinformatics (5 stars, last pushed 2mo ago), with no licence file. It adds 63 tokens to every session and 1,849 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.