protein-msa

name	protein-msa
description	Align multiple protein sequences with EBI Clustal Omega to assess similarity and residue/domain conservation (up to 4000 sequences, 4 MB). Not for homolog search, non-protein sequences, structural alignment, or a single sequence. Public EBI API, no credential needed.
license	Apache-2.0

Protein Msa (Codex-native)

Codex-native adaptation of Google DeepMind's protein-sequence-msa skill (science-skills, Apache-2.0). Uses the public API directly through Codex's own tools.

Gates (ask before proceeding)

• Terms notice: on first use in a workspace, tell the user to review the source's terms of use and record the notice in provenance.
• Network / install: read-only public access; be polite about rate limits. Write large responses to a file and parse them; if you write helper code, run it via uv run, never bare python3. Ask before installs or large downloads.

Endpoints

• EBI Clustal Omega REST https://www.ebi.ac.uk/Tools/services/rest/clustalo/

Workflow

1. Submit the FASTA of >=2 protein sequences (/run), poll /status/<jobId>, then fetch results (/result/<jobId>/...).
2. Report conserved columns/regions and key-residue conservation from the alignment.

• Provenance & review: record queries, endpoints, and cited identifiers with $science-provenance; check claims with $science-review before presenting.

Boundaries

• This aligns given sequences; it does not find homologs (use $cx-protein-similarity-search).
• Respect the size limits and EBI rate limits; cite the job/inputs used.