bio-remote-homology SKILL.md skillA
bio-remote-homology from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-remote-homology@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-database-access-remote-homology/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 18,802 bytes
- Repository stars
- 662
- License
- MIT
Detect distant homologs using profile and structure-aware methods that go beyond standard BLAST. Use when sequence identity falls into the twilight zone (<35% pairwise), when BLAST fails to find homologs that should exist, when working at metagenomic scale (DIAMOND, MMseqs2), or when structure beats sequence (Foldseek). Covers PSI-BLAST (iterative PSSM), jackhmmer (iterative HMM), HHblits/HHsearch (profile-profile), DIAMOND, MMseqs2, and Foldseek (3Di structural alphabet, van Kempen 2024).
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## Version Compatibility Reference examples tested with: NCBI BLAST+ 2.15+, HMMER 3.4+, MMseqs2 15+, DIAMOND 2.1+, HH-suite3 3.3+, Foldseek 9+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags - Python: `pip show <package>` then introspect signatures If a flag is unrecognized or behavior changes, introspect with `--help` and adapt the example to match the installed version rather than retrying. # Remote Homology **"Find homologs my BLAST missed"** -> Standard BLAST detects similarity reliably down to ~35% pairwise identity (the "twilight zone", Rost 1999 *Protein Eng* 12:85). Below that, profile methods (PSSMs, HMMs) and structure-aware methods (Foldseek) recover homologs that pairwise alignment misses. …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-remote-homology@sha256:d6b54c4b80774a11The line at the top of this page pins the label git:20260821.2d1b678, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_2pypimlqaiomkfvt)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
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- pass: No link to an exfiltration or paste host
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- pass: No instruction to read or print local credentials
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- pass: No script tag
Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_2pypimlqaiomkfvt GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-remote-homology GET https://markdownregistry.com/api/v1/blob/d6b54c4b80774a112446736b39db8b96454a34839c7fa27552a2e173ecbb2c3f
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.