clustalo-msa

name	clustalo_msa
description	Multiple sequence alignment of proteins via EBI Clustal Omega web service. Use when you have ≥2 protein sequences in a FASTA file (≤4000 sequences, ≤4 MB) and need an alignment to assess conservation, residue importance, or domain structure. Do NOT use for: single sequences, homology search (use protein_sequence_similarity_search), structural alignment (use foldseek), or DNA/RNA alignment.

Clustal Omega MSA (EBI)

Overview

Submits a FASTA file with multiple protein sequences to the EBI Clustal Omega REST service, polls for completion, and downloads the resulting alignment in FASTA format. Pipeline is fully managed by the tool — the agent only provides the input FASTA and an output directory.

Project Tools (VenusFactory2)

Tool	Args	Returns	Description
download_clustalo_msa_by_fasta	fasta_path (required, path to input FASTA), out_dir (required), email (optional; falls back to env USER_EMAIL, then [e-mail]), poll_interval (default 10.0 s), timeout_secs (default 900 s)	JSON: {status, file_info {file_path, file_name, file_size, format: "fasta"}, content_preview, biological_metadata {input_sequences, aligned_sequences, job_id, email}, execution_context}	Submit + poll + download MSA. Writes <input_stem>_msa.fasta to out_dir.

When to Use This Skill

• Compute MSA for a small/medium set of homologous proteins (UniProt search results, BLAST hits, manually curated set)
• Generate input for conservation scoring, phylogenetic analysis, or HMM profile training
• Identify conserved active-site residues from a small protein family

When NOT to Use

• Single sequence input → use protein_sequence_similarity_search to first find homologs

• 4000 sequences or >4 MB FASTA → EBI rejects; split into chunks or run locally with mafft --auto

• DNA / RNA alignment → Clustal Omega is for proteins
• Structural alignment of 3D structures → use download_foldseek_results_by_pdb_file

Pipeline

1. Validate input: file exists, size ≤ 4 MB, 2 ≤ sequence count ≤ 4000.
2. Submit: POST https://www.ebi.ac.uk/Tools/services/rest/clustalo/run with email + title + sequence form data.
3. Poll: GET .../status/{job_id} every poll_interval seconds until FINISHED (or ERROR/FAILURE/NOT_FOUND → fail fast).
4. Download: GET .../result/{job_id}/fa → FASTA alignment text.
5. Save: write to <out_dir>/<input_stem>_msa.fasta.

Rate Limiting & Politeness

• The tool defaults to 10-second polls with a 15-minute wall-clock timeout.
• EBI requests a valid contact email — the default [e-mail] works but setting USER_EMAIL in your environment is preferred so EBI can contact you if your job affects service health.
• A single submit + many polls is the established contract; do not invoke the tool in a tight loop.

Common Mistakes

• Passing a single sequence: the tool errors with ValidationError: need ≥2 sequences. Run a similarity search first.
• Pasting raw sequences into a tool argument: this tool only accepts a file path. Write the FASTA to disk first (use read_fasta, extract_uids_from_fasta, etc., to compose).
• Mixing nucleotide and protein sequences: EBI returns garbage. Filter the input FASTA before calling.

References

• EBI Clustal Omega REST docs
• Terms of use
• Adapted from google-deepmind/science-skills:skills/protein_sequence_msa/scripts/msa_align.py