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Get Started Free →mkurman/ncbi-sequence-fetch
Retrieve protein and nucleotide sequences from NCBI databases using E-utilities. Supports direct accession lookup, CDS translation, gene+organism search, locus lookup, PubMed-linked sequences, patent protein extraction, and organism+length fallback search.
6 of 22 test cases passed with the skill.
Tokens, turns and time describe resource use, not a dollar price.
Lift withheld: 5 comparable cases; this report requires 8.
One of 2 test cases the skill fixed. Same model, same prompt, with and without the skill.
We are analyzing Arabidopsis thaliana gene locus At1g56540. What command fetches the protein sequence associated with this locus tag?
| Checked | Without skill | With skill |
|---|---|---|
| The command executes scripts/ncbi_fetch.py locus-protein At1g56540 --organism "Arabidopsis thaliana". | Missed | Passed |
The instructions your model reads when the skill loads.
uv: Read the uv skill and follow its Setup instructions to ensure
uv is installed and on PATH.
User Notification: If LICENSE_NOTIFICATION.txt does not already exist in this skill directory then (1) prominently notify the user to check the terms at https://www.ncbi.nlm.nih.gov/ and https://www.ncbi.nlm.nih.gov/home/about/policies/, then (2) create the file recording the notification text and timestamp.
.env file: Make sure the .env file exists in your home directory.
Create one if it does not exist.
NCBI_API_KEY (optional): Raises the NCBI rate limit from 3 to 10
requests/second. The skill works without it, but a key is recommended if the
user plans many queries or encounters a 429 error. The user can obtain one
for free by registering at https://www.ncbi.nlm.nih.gov/account/settings/.
If the variable is missing from .env, do NOT ask the user to paste it into
the chat (this would leak the key into the agent's context). Instead, give
the user this command — substituting ENV_FILE with the resolved literal
path to the .env file:
printf "Enter NCBI API key (typing hidden): " && read -s key && echo && echo "NCBI_API_KEY=$key" >> "ENV_FILE" && echo "Saved."
The scripts load credentials automatically via dotenv. NEVER read,
print, or inspect the .env file or its variables (e.g. no cat, grep,
echo, printenv, or os.environ.get on keys). Credentials must stay out
of the agent's context.
NCBI_API_KEY in their
environment, the query speed limits are automatically increased
significantly.test cases passed with the skill
More skills from the same source and nearby in the registry, with their headline benchmark lift.