Protein Sequence Similarity Search
Searches for homologous protein sequences using MMseqs2 (fast, default) or BLAST...
Install
npx skills add google-deepmind/science-skills --skill protein-sequence-similarity-search -g -a claude-code -y- Repository
- google-deepmind/science-skills3.4k
- Category
- Engineering
- Updated
- 12d ago
- License
- Apache-2.0
- Context cost
- Mediumabout 2,552 tokens
- Runs scripts
- Yes, review before use
What it does
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.
Prerequisites
uv: Read theuvskill and follow its Setup instructions to ensureuvis installed and on PATH.- 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.
.envfile: Make sure the.envfile exists in your home directory. Create one if it does not exist.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 thecredentialsskill 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.
