Agent skill · research science · google-deepmind
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.
Why this skill is useful
Adds specific commands and workflows for using MMseqs2 and BLAST for protein sequence similarity searches, which the AI wouldn't reliably generate on its own.
What it needs
Requires uv installed locally. About 6k tokens when loaded. Last updated 2026-07-07. 2,648 stars on the source repository.
What this skill does
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/proteinsequencesimilaritysearchLICENSE.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. USEREMAIL (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 Strict Validation: For BLAST, only use database codes listed in the table below. No Hallucinations: If a script throws an error or returns no hits, inform the user clearly. Do NOT invent sequence homologues. Do Not Parse Output Files: Do not parse the JSON, a3m, or any other raw output files. Rely on the generated .md file for your summary. The JSON and other outputs are for subsequent tool use only. Always State the Method: Every report must clearly state whether the search used the quick MMseqs2 (ColabFold API) or the slower EBI BLAST method. Notification: If this skill is used, ensure this is mentioned in the output. Explicitly state that the corresponding program (MMSEQS2 or EBI BLAST) and Sequence Databases were used. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills google-deepmind/protein_sequence_similarity_search