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Agent Skill

Msa Search Nim skill

msa-search-nimNVIDIA/skillsskills/bionemo-msa-search-nim/SKILL.md

Generate multiple sequence alignments (MSAs) for protein sequences using the ColabFold MSA-Search NIM. Use for homolog search, UniRef30/ColabFold env searches, A3M or FASTA alignments, paired MSA search for complexes, PDB70 structural templates, hosted NVIDIA API calls, or local Docker deployment. For local deployment, download the databases in parallel with aria2c and launch via NIM_MODEL_NAME (the recommended default fast path, ~14 min vs over 80 min for the built-in downloader); a plain docker run uses the slow built-in downloader.

3.7kApache-2.0

always on

128 tokname + description

once used

4,783 tokSKILL.md body

bundled files

142 scripts

repo stars

3.7kGitHub

Install the Msa Search Nim skill

Skills CLI (Claude Code, Codex, Cursor and others)

npx skills add https://github.com/NVIDIA/skills --skill msa-search-nim

Claude Code, by hand (all projects)

git clone --depth 1 https://github.com/NVIDIA/skills.git /tmp/skills
mkdir -p ~/.claude/skills
cp -R /tmp/skills/skills/bionemo-msa-search-nim ~/.claude/skills/msa-search-nim

For one project only, copy the folder into .claude/skills/ in that project instead. The agent picks it up when a task matches its description.

What it costs your context

Agent Skills load in three steps. Tokens counted with the o200k tokenizer; your model's count will differ a little.

WhenWhat loadsCost
Every sessionName and description128 tok
When the agent uses itThe SKILL.md instructions4,783 tok
Only if opened14 bundled files (67 KB)varies

Until it is used, msa-search-nim costs about 11× less than the median MCP server we measured (1,363 tokens on every turn). Installing all 150 skills from NVIDIA/skills would load 20,796 tokens of descriptions. Skills vs MCP study

Checks

  • Ships scripts the agent can run. Read them before installing.
  • The name doesn't match its folder name, as the specification requires.

Pre-approved tools (allowed-tools): Bash, Read, Write, AskUserQuestion. The agent can use these without asking while the skill is active.

Checked 2026-10-22 · method

What's inside

The headings of its SKILL.md. Read the full file on GitHub.

  • MSA-Search NIM
  • Choose Mode And Endpoint
  • Local Docker
  • Fallback: Let The NIM Download Its Own Databases (slower)
  • Faster Startup: Task-Specific Database Profiles
  • Custom Or Individual Databases
  • Recommended: Parallel Download For Any Database Set (Fast Deployment)
  • Standard MSA Request
  • Paired MSA Request
  • Local Template Search
  • Save Outputs
  • Limits And Troubleshooting

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