Ncbi Sequence

Organization

ai4protein

ncbi_sequence

NCBI E-utilities for biological sequences — fetch protein/nucleotide FASTA by accession, run BLAST, translate CDS to protein, search NCBI Protein by gene+organism. Use when the user provides an NCBI accession (NP_, XP_, NM_, NR_, etc.), asks for a sequence by gene name + species, or needs to translate a coding sequence. Don't use for ClinVar variants (use ncbi_clinvar) or gene metadata lookup (use ncbi_gene).

Overview

Publisher	ai4protein
Repository	`VenusFactory2`
Skill name	`ncbi_sequence`
Stars	255
Forks	37
Bundled files	Instructions only
License	Unknown
Links	Skill source Repository Homepage

Markdown instructions
A SKILL.md file the model loads on demand, so it only costs tokens when a request actually matches.
Works with any LLM
AI skills are plain Markdown, not provider-specific code, so this works with GPT, Claude, Gemini, Grok, or a local model.
Self-contained
Everything the model needs lives in the instructions — no extra files to sync.
Open source
Published by ai4protein on GitHub. Read the source before you install it.

Installation

Install the Ncbi Sequence AI skill in TypingMind to use it with any LLM, or drop it into another agent that reads SKILL.md.

Install in TypingMind

TypingMind installs a skill straight from its GitHub folder — it reads SKILL.md, bundles the resource files, and stores the result locally.

Open the app and go to Plugins → Skills.
Choose "Install from GitHub".
Paste the skill folder URL below and confirm.
https://github.com/ai4protein/VenusFactory2/tree/main/src/agent/skills/ncbi_sequence
Enable the skill in any chat where you want it available.

Plugins → Skills → Add skill → From GitHub URL, then paste the folder URL and press Continue.

Install in another agent

Any agent that reads the Agent Skills format can use this skill — copy the folder into that agent's skills directory.

Claude Code — .claude/skills

git clone --depth 1 https://github.com/ai4protein/VenusFactory2.git /tmp/VenusFactory2
mkdir -p .claude/skills
cp -r /tmp/VenusFactory2/src/agent/skills/ncbi_sequence .claude/skills/ncbi_sequence

Restart Claude Code after copying so it picks up the new skill.

Use it in TypingMind

Enable Ncbi Sequence in any TypingMind chat and the model takes it from there. Its name and description sit in the system prompt, and the moment a request matches, the model loads the full instructions itself — you never invoke it by hand, and it costs no tokens until it is actually used.

The model loads Ncbi Sequence on its own as soon as a request matches it.

Works with any AI model

AI skills are plain Markdown instructions rather than provider-specific code, so Ncbi Sequence is not tied to the model it was written for. Install it once in TypingMind and use it with GPT-5, Claude, Gemini, Grok, DeepSeek, Mistral, Llama, or a local model you run yourself — all on your own API keys.

Loaded only when it is needed
The system prompt carries just the name and description. The instructions are fetched on the first matching request, so an idle skill costs nothing.
Switch models mid-chat
Because the skill is instructions rather than code, changing model does not break it — the next model reads the same SKILL.md.

Skill instructions

This is the SKILL.md content the model loads. Read it before installing — a skill is instructions your model will follow.

NCBI Sequence Tools

Overview

Wraps NCBI E-utilities (efetch, esearch) for sequence-centric workflows. Honors NCBI_API_KEY env var to raise the QPS limit from 3 → 10. Set USER_EMAIL env var to identify yourself to NCBI as a good citizen.

Project Tools (VenusFactory2)

Tool	Args	Returns	Description
download_ncbi_sequence	`ncbi_id`, `out_dir`, `db` (default `protein`)	rich JSON envelope; FASTA file	Fetch a single sequence by accession from `protein` or `nuccore`.
download_ncbi_metadata	`ncbi_id`, `out_path`, `db`	rich JSON envelope; metadata JSON	Fetch GenBank-style metadata for an accession.
download_ncbi_blast	(see existing schema)	rich JSON envelope	NCBI-hosted BLAST. Prefer `download_mmseqs2_homologs_by_sequence` (faster) or `download_blast_homologs_by_sequence` (EBI mirror) for protein-protein searches.
translate_ncbi_cds_to_protein	`accession` (nuccore, e.g. `NM_000518` for HBB mRNA), `out_dir`, `target_length` (default `0` = longest), `timeout`	rich JSON envelope; FASTA at `<out_dir>/<accession>_protein.fasta`; `biological_metadata.method="fasta_cds_aa"`	Use `efetch(rettype=fasta_cds_aa)` to get the CDS-translated protein, pick the translation closest to `target_length` (or longest).
search_ncbi_protein_by_gene_and_organism	`gene` (e.g. `TP53`), `organism` (`"Homo sapiens"`), `out_dir`, `target_length` (default `0` = no length filter; non-zero filters to ±25 aa window), `retmax` (default `10`), `timeout`	rich JSON envelope; multi-FASTA + `<stem>.json` summary; `biological_metadata.summary_path` for the per-hit JSON	Search NCBI Protein DB with `<gene>[Gene Name] AND <organism>[Organism]`, fetch all hits as multi-FASTA.

Workflow: "Get the protein sequence for gene X in species Y"

Try search_ncbi_protein_by_gene_and_organism first — if it finds 1-5 hits, pick the canonical one.
If you know the mRNA accession (e.g. from a Gene record), use translate_ncbi_cds_to_protein for the canonical CDS-derived protein (no ambiguity from isoforms).
Fallback: keyword search via download_ncbi_metadata to find an accession, then download_ncbi_sequence.

Workflow: "Translate this mRNA to protein"

Direct: translate_ncbi_cds_to_protein(accession=..., target_length=expected_aa_count). The tool uses NCBI's pre-translated CDS protein when available — no client-side translation needed, no codon-table issues.

Common Mistakes

Confusing protein and nuccore DBs: protein accessions (NP_, XP_, AAA-style) go to db=protein; mRNA/genomic (NM_, NC_, etc.) go to db=nuccore. translate_ncbi_cds_to_protein always uses nuccore internally.
Mismatched gene+organism: NCBI is strict; TP53 AND Homo sapiens works, tp53 AND human may not.
Forgetting NCBI_API_KEY: at 3 QPS you'll hit rate limits with batch operations. Set the env var to bump to 10 QPS.
target_length too narrow: search_ncbi_protein_by_gene_and_organism applies ±25 aa filter; if your target_length is uncertain, pass 0 and pick from results.

Frequently asked questions

What does the Ncbi Sequence AI skill do?

Why use Ncbi Sequence on TypingMind?

Because you install it once and use it with any model. Ncbi Sequence is plain Markdown rather than provider-specific code, so the same skill runs on GPT-5, Claude, Gemini, Grok, or a local model — and you can switch model mid-chat without it breaking. TypingMind runs on your own API keys, so you pay providers directly instead of a per-seat subscription, and your skills and chats stay in your own storage.

How do I install Ncbi Sequence in TypingMind?

Open Plugins → Skills → Install from GitHub in TypingMind and paste https://github.com/ai4protein/VenusFactory2/tree/main/src/agent/skills/ncbi_sequence. TypingMind reads its SKILL.md and installs it as a skill you can enable per chat.

Which AI models can use Ncbi Sequence?

Any model you connect in TypingMind. AI skills are plain Markdown instructions rather than provider-specific code, so GPT, Claude, Gemini, Grok, and local models can all load this skill when a request matches it.

How many AI models can I use with Ncbi Sequence?

As many as you like. As long as a model supports skills, you can use Ncbi Sequence with it — GPT, Claude, Gemini, Grok, DeepSeek, Mistral, Llama and more — all on TypingMind with your own API keys.

Is the Ncbi Sequence AI skill free?

Yes. It is published on GitHub by ai4protein under the Unknown license. You only pay your own AI provider for the tokens you use.

What are AI skills?

An AI skill is a reusable instruction bundle that teaches an AI model how to do one specific task. It follows the open Agent Skills format: a SKILL.md file with a name and description, plus any scripts, templates or reference files the model may need. The model reads the instructions only when your request matches the skill, so an installed skill costs nothing until it is used.

How are AI skills different from plugins or MCP servers?

A plugin or MCP server gives a model new tools to call — code that runs somewhere and returns a result. An AI skill gives the model knowledge and process instead: how to approach a task, which steps to follow, what good output looks like. Skills are plain Markdown, so they need no server, no API key and no runtime, and they work with any model.

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Overview

Installation

Install in TypingMind

Install in another agent

Use it in TypingMind

Works with any AI model

Skill instructions

NCBI Sequence Tools

Overview

Project Tools (VenusFactory2)

Workflow: "Get the protein sequence for gene X in species Y"

Workflow: "Translate this mRNA to protein"

Common Mistakes

References

Frequently asked questions

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