Individual skill
msa-search-nim
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.
skills/bionemo-msa-search-nim/SKILL.md
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# MSA-Search NIM
Generate protein MSAs with GPU-accelerated MMSeqs2. Use this guide for
first-pass hosted/local usage; load supplemental files only when needed:
- `references/api.md`: exact endpoints, schemas, Docker flags, response fields.
- `references/science.md`: MSA purpose, pairing/templates, limits, handoffs.
- `references/parameters.md`: database, pairing, depth, and template tuning.
- `references/validation.md`: alignment, template, and artifact checks.
- `references/examples.md`: compact hosted/local request patterns.
## Choose Mode And Endpoint
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