Individual skill

protein-sequence-similarity-search

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.

skills/protein_sequence_similarity_search/SKILL.md

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Last checked: Nov 2, 2026

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Repository stars (not skill ratings): 3,431
Repository last updated: Oct 23, 2026
License: Apache-2.0

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engineering Derived category

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SKILL.mdcore · 10,728 bytes
references/citation.bibasset · 2,128 bytes
scripts/mmseqs2_search.pyruns · 11,107 bytes
scripts/uniprot_blast.pyruns · 9,033 bytes

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## 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