bio-local-blast SKILL.md skillA
bio-local-blast 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-local-blast@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-local-blast/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 16,517 bytes
- Repository stars
- 662
- License
- MIT
Build local BLAST databases and run searches using NCBI BLAST+ command-line tools. Use when running >50 queries, building custom databases with -parse_seqids and -taxid, downloading prebuilt NCBI databases via update_blastdb.pl, choosing -task variants (megablast/dc-megablast/blastn/blastn-short), tuning soft/hard masking, scaling threads, or extracting hits with blastdbcmd. Encodes BLAST v5 vs v4 database format, taxonomy filtering, makeblastdb pitfalls.
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+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `blastn -version` then `blastn -help` to confirm flags - CLI: `makeblastdb -help` to confirm database build options If a flag is unrecognized or behavior changes, introspect with `-help` and adapt the example to match the installed version rather than retrying. # Local BLAST **"Run BLAST locally for speed and control"** -> Build or download a BLAST+ database, run the appropriate program with carefully chosen `-task`, masking, and thread settings, parse tabular output. Local BLAST is the right tool when remote is rate-limited or when the database must be reproducible (frozen). The biggest mistakes are (a) using `nt`/`nr` without realizing they're >250 GB and grow weekly, (b) not building with `-parse_seqids` and then being unable to extract hit sequences with `blastdbcmd`, (c) using default `blastn` for cross-species when `dc-megablast` is correct, and (d) thinking `-num_threads 32` will scale -- past ~16 threads BLAST is I/O bound. …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-local-blast@sha256:e5c8078ed0a92e4cThe 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_lebjfitpdczf3pyo)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
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- pass: Size between 200 bytes and 200 KB (16517 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- 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_lebjfitpdczf3pyo GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-local-blast GET https://markdownregistry.com/api/v1/blob/e5c8078ed0a92e4c6baf01975e06ddeea1682a063fa75776a00783585c738397
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.