# Protein Sequence Similarity Search

Searches for homologous protein sequences using MMseqs2 (fast, default) or BLAST...

- Repository: https://github.com/google-deepmind/science-skills (3377 stars)
- Category: Engineering
- License: Apache-2.0
- Last updated: 2026-10-23
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add google-deepmind/science-skills --skill protein-sequence-similarity-search -g -a claude-code -y`
Codex: `npx skills add google-deepmind/science-skills --skill protein-sequence-similarity-search -g -a codex -y`
Cursor: `npx skills add google-deepmind/science-skills --skill protein-sequence-similarity-search -g -a cursor -y`
Gemini CLI: `npx skills add google-deepmind/science-skills --skill protein-sequence-similarity-search -g -a gemini-cli -y`

## Description

Searches for homologous protein sequences using MMseqs2 (fast, default) or BLAST (comprehensive, fallback). Trigger this whenever the user provides a protein sequence or FASTA file and asks to find homologues, sequence matches, or wants to infer protein function based on sequence similarity, but not when the user wants to infer protein function based on structural similarity.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

## Prerequisites

1.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
    `uv` is installed and on PATH.
2.  **User Notification**: If
    .licenses/protein_sequence_similarity_search_LICENSE.txt does not already
    exist in the workspace root directory then (1) prominently notify the user
    to check the terms at https://www.ebi.ac.uk/jdispatcher/sss/ncbiblast and
    https://colabfold.com, then (2) create the file recording the notification
    text and timestamp.
3.  **`.env` file**: Make sure the `.env` file exists in your home directory.
    Create one if it does not exist.
4.  **`USER_EMAIL`** (optional but recommended): Recommended by the EBI for
    BLAST job tracking, but the skill works without it. You **MUST** use the
    safe credentials protocol in the `credentials` skill to check for and
    request this credential if this skill looks relevant to the user's request.

## Goal

Take a user-provided amino acid sequence (or a path to a `.fasta` file), search
for sequence homologues using the fastest available method, generate a
Markdown-formatted table of the top hits, interpret key alignment metrics,
summarize the inferred protein functions, and save results locally for future
programmatic analysis.

## Core Rules

The rest: https://github.com/google-deepmind/science-skills/blob/HEAD/skills/protein_sequence_similarity_search/SKILL.md