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Protein Sequence Msa

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Multiple sequence alignment for proteins using the EBI Clustal Omega web service.

What it does

Protein Sequence Msa enables your assistant to perform scientific alignment tasks by connecting to the EBI Clustal Omega API. Once configured, your assistant gains the ability to process FASTA files to identify conserved regions and assess similarity across multiple protein chains.

By automating the interaction with this external service, the assistant ensures that alignment requests follow established usage guidelines. This allows you to focus on the biological interpretation of the alignment data rather than managing the mechanics of the request or the raw output file structure.

When it earns its place

Reach for it when…

Apply this when you have a FASTA file containing two or more protein sequences and need to evaluate how specific residues or domains are conserved across that group.

Look elsewhere when…

Do not use this for searching databases to find homologs or for structural alignments involving 3D coordinates, as this tool is strictly limited to sequence-based global alignment.

What to say to use it

You never invoke a skill directly — the assistant picks it up when your request matches what it covers. These are the kinds of things that do that.

  • Align these three protein sequences in this file
  • Show me the conserved domains across my protein set
  • Calculate the identity metrics for these FASTA sequences
  • Run an alignment on these proteins using Clustal Omega

Install it

Install for all your projects

Copy the skill directory into your personal skills folder. Claude picks it up on its own the next time your request matches what it does — there is nothing to enable.

bash
git clone --depth 1 --branch main https://github.com/google-deepmind/science-skills.git /tmp/science-skills
mkdir -p ~/.claude/skills
cp -r /tmp/science-skills/skills/protein_sequence_msa ~/.claude/skills/protein-sequence-msa

Install for one project only

Put it in the project's own skills folder instead, so it can be committed and shared with everyone working on that repository.

bash
cp -r /tmp/science-skills/skills/protein_sequence_msa .claude/skills/protein-sequence-msa

If a skill of the same name exists in both places, the personal one wins.

Installing on Claude.ai or through the API instead? The full guide covers every surface.

Pair it with an MCP server

Protein Sequence Msa changes how the work is done. These servers change what Claude can reach while doing it.

How skills and MCP servers differ →