Protein Sequence Msa
Performs multiple sequence alignment of proteins with EBI Clustal Omega.
Install
npx skills add google-deepmind/science-skills --skill protein-sequence-msa -g -a claude-code -y- Repository
- google-deepmind/science-skills3.4k
- Category
- Data and ML
- Updated
- 12d ago
- License
- Apache-2.0
- Context cost
- Lightabout 1,396 tokens
- Runs scripts
- Yes, review before use
What it does
Performs multiple sequence alignment of proteins with EBI Clustal Omega. Use when you need to align multiple sequences to assess similarity, domain conservation, or key residue conservation. Supports up to 4000 sequences and a maximum file size of 4 MB. Do not use to search for homologous proteins in a database (use MMseqs2, BLAST), align non-protein sequences (DNA, RNA), perform structural alignment (use Foldseek, PyMOL), or if you only have a single sequence.
Prerequisites
uv: Read theuvskill and follow its Setup instructions to ensureuvis installed and on PATH.- User Notification: If .licenses/protein_sequence_msa_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/msa/clustalo and https://www.ebi.ac.uk/about/terms-of-use/, 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: Required by the wrapper script for Clustal Omega job tracking (recommended by the EBI). 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.
Core Rules
- Use the Wrapper: ALWAYS execute the alignment using
scripts/msa_align.pyrather than writing your own curl or custom Python requests. The script automatically enforces the required rate limit to respect EBI's Terms of Use. - Notification: If this skill is used, ensure this is mentioned in the output.
- Always state the method: Every report must clearly state that the alignment was performed using EBI Clustal Omega.
- No Hallucinations: Do NOT invent alignments or conservation metrics. Report only what is present in the alignment file.
Goal
Take a file containing multiple protein sequences in FASTA format, perform multiple sequence alignment using the EBI Clustal Omega API, save the resulting alignment locally for future programmatic analysis, and interpret the results towards addressing the user's specific research objective (e.g., assessing similarity, identifying conserved domains, or analyzing key residues).
