Agent skill

Blast

Search NCBI BLAST for sequence homology and find similar sequences in biological databases

Apache-2.0Auto-check passedResearch & Science

Install Blast

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill blast -a claude-code

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

GitHub CLI

$ gh skill install lamm-mit/scienceclaw blast --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/lamm-mit/scienceclaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/blast .claude/skills/blast && 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/

Paste into Claude Code

Install the "blast" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/blast into .claude/skills/blast/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "blast", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/lamm-mit/scienceclaw/tree/main/skills/blast

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill blast -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw blast --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/blast .agents/skills/blast && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "blast" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/blast into .agents/skills/blast/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "blast", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill blast -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw blast --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/blast .cursor/skills/blast && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "blast" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/blast into .cursor/skills/blast/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "blast", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/lamm-mit/scienceclaw.git --path skills/blast

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill blast -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw blast --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/blast .gemini/skills/blast && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "blast" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/blast into .gemini/skills/blast/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "blast", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw blast

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill blast -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/blast .github/skills/blast && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "blast" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/blast into .github/skills/blast/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "blast", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill blast -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw blast --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/blast .opencode/skills/blast && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "blast" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/blast into .opencode/skills/blast/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "blast", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: blast
GitHub stars: 244
Token cost: ~758 tokens
SKILL.md length: 255 words
Files: 3 (incl. scripts)
Skills in repo: 85
Repo updated: Aug 21, 2026
First seen: Oct 7, 2026
Licence: Apache-2.0

At a glance

Search NCBI BLAST for sequence homology and find similar sequences in biological databases

Research & Science work in your project
SKILL.md covers Overview, Usage, Parameters and BLAST Programs, plus 4 more sections
Runs Python scripts from its folder; calls python3

What it does

Blast is an agent skill from lamm-mit/scienceclaw. Search NCBI BLAST for sequence homology and find similar sequences in biological databases

Its SKILL.md is about 760 tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files, including scripts (for example `scripts/blast_search.py`).

It sits in Research & Science. It works with NCBI. The licence is Apache-2.0.

When your agent uses it

Research & Science work in your project

Example prompts

“/blast”

Requirements

Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit ab9aba1. 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 2 files in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
- python3
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
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

Blast loads about 758 tokens when it runs. Until then it costs about 24 tokens; SKILL.md has 255 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~24
When it runs · the whole SKILL.md, loaded when a task matches: ~758

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); the scripts in this folder are not scanned.

SKILL.md

The full file from lamm-mit/scienceclaw at commit ab9aba1, republished under its Apache-2.0 licence (© lamm-mit). 255 words, ~758 tokens.

Download SKILL.mdSave it as .claude/skills/blast/SKILL.md (or your agent's skills folder). This skill also uses 2 other files; get the full folder from GitHub.

name: blast
description: Search NCBI BLAST for sequence homology and find similar sequences in biological databases

BLAST Search

Run NCBI BLAST (Basic Local Alignment Search Tool) searches to find sequence homology against NCBI databases.

Overview

BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.

Usage

Basic protein BLAST search:

bash

python3 {baseDir}/scripts/blast_search.py --query "MTEYKLVVVGAGGVGKSALTIQLIQ" --program blastp

Nucleotide search:

bash

python3 {baseDir}/scripts/blast_search.py --query "ATGCGATCGATCGATCG" --program blastn

Search from FASTA file:

bash

python3 {baseDir}/scripts/blast_search.py --query /path/to/sequence.fasta --database nr --program blastp

Get detailed output:

bash

python3 {baseDir}/scripts/blast_search.py --query "SEQUENCE" --program blastp --format detailed --max-hits 20

Parameters

Parameter	Description	Default
`--query`	Amino acid/nucleotide sequence or path to FASTA file	Required
`--program`	BLAST program: blastn, blastp, blastx, tblastn, tblastx	blastp
`--database`	Database to search: nr, nt, refseq_protein, refseq_rna, swissprot, pdb	nr
`--evalue`	E-value threshold	10.0
`--max-hits`	Maximum number of hits to return	10
`--format`	Output format: summary, detailed, json	summary

BLAST Programs

blastp: Protein query vs protein database
blastn: Nucleotide query vs nucleotide database
blastx: Translated nucleotide query vs protein database
tblastn: Protein query vs translated nucleotide database
tblastx: Translated nucleotide query vs translated nucleotide database

Databases

nr: Non-redundant protein sequences
nt: Non-redundant nucleotide sequences
refseq_protein: NCBI Reference Sequence protein database
refseq_rna: NCBI Reference Sequence RNA database
swissprot: Swiss-Prot protein database (curated)
pdb: Protein Data Bank sequences

Examples

Find similar proteins to human p53:

bash

python3 {baseDir}/scripts/blast_search.py --query "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP" --program blastp --database swissprot

Search for homologs with strict E-value:

bash

python3 {baseDir}/scripts/blast_search.py --query "MTEYKLVVVGAGGVGKSALTIQLIQ" --evalue 0.001 --max-hits 50

Output

The tool returns:

Hit accession and description
E-value and bit score
Percent identity and alignment length
Query and subject coverage
Alignment details (in detailed mode)

Notes

BLAST searches are submitted to NCBI servers and may take 30 seconds to several minutes
For large-scale searches, consider using local BLAST+ installation
NCBI requests that you provide an email for heavy usage (set NCBI_EMAIL environment variable)

Files

SKILL.md and 2 other files (scripts) in skills/blast of lamm-mit/scienceclaw.

SKILL.md
scripts/__pycache__/blast_search.cpython-313.pyc
scripts/blast_search.py

Open the folder on GitHubat commit ab9aba1

Compare with similar skills

Blast next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Blast compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Blast this skilllamm-mit/scienceclaw	244	—	~758	Automated safety check: Pass	Apache-2.0	1 mo ago
Dbsnp Databasegoogle-deepmind/science-skills	3.2k	3 repos	~3.4k	Automated safety check: Notes	Apache-2.0	22 days ago
Biopython Bioinformaticsaiming-lab/AutoResearchClaw	15k	—	~810	Automated safety check: Pass	MIT	1 mo ago
Bio Write SequencesGPTomics/bioSkills	1.2k	3 repos	~2.1k	Automated safety check: Pass	MIT	1 mo ago
Mako Loreliebaojun/MakoCode	155	—	~692	Automated safety check: Pass	Custom licence	1 mo ago
PubMed REST API Searchdavila7/claude-code-templates	32k	15 repos	~3.9k	Automated safety check: Pass	MIT	today

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Biopython Bioinformatics
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Quick reference for Biopython work: sequence operations, SeqIO file parsing, BLAST searches, Entrez queries, phylogenetic trees and PDB structure analysis.
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Research & ScienceAuto-check passed
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Questions about Blast

What does Blast do?

Search NCBI BLAST for sequence homology and find similar sequences in biological databases. Blast is an agent skill from lamm-mit/scienceclaw.

When should I use Blast?

Blast fits situations like: research & Science work in your project.

How do I install Blast in Claude Code?

Run `npx skills add lamm-mit/scienceclaw --skill blast -a claude-code`. Or copy the skill folder (skills/blast in lamm-mit/scienceclaw) into .claude/skills/blast in your project. Claude Code loads it when a task matches its description.

How do I install Blast in Codex?

Run `npx skills add lamm-mit/scienceclaw --skill blast -a codex`. Or copy the skill folder (skills/blast in lamm-mit/scienceclaw) into .agents/skills/blast in your project. Codex loads it when a task matches its description.

Can I use Blast 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 lamm-mit/scienceclaw --skill blast -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/blast, .gemini/skills/blast, .github/skills/blast and .opencode/skills/blast in your project.

What does Blast need to run?

Going by SKILL.md and its folder, Blast needs Python for the scripts in its folder and the command-line tools its instructions call (python3). Our summary lists: Python 3.

Does Blast access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Blast 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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Blast use?

Blast is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Blast use?

About 758 tokens (SKILL.md is roughly 3k 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 Blast?

Skills that share tags, products or a category with Blast: Dbsnp Database (google-deepmind/science-skills, 3.2k stars), Biopython Bioinformatics (aiming-lab/AutoResearchClaw, 15k stars), Bio Write Sequences (GPTomics/bioSkills, 1.2k stars) and Mako Lore (liebaojun/MakoCode, 155 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Blast?

lamm-mit (a GitHub user) maintains it in lamm-mit/scienceclaw, which has 244 GitHub stars. The repository holds 85 skills in this directory. The repository was last updated on August 21, 2026.

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

Install Blast

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

BLAST Search

Overview

Usage

Basic protein BLAST search:

Nucleotide search:

Search from FASTA file:

Get detailed output:

Parameters

BLAST Programs

Databases

Examples

Find similar proteins to human p53:

Search for homologs with strict E-value:

Output

Notes

Files

Compare with similar skills

Similar skills

More from lamm-mit/scienceclaw

Related

Questions about Blast