bio-blast-searches SKILL.md skillA
bio-blast-searches 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-blast-searches@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-blast-searches/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 15,778 bytes
- Repository stars
- 662
- License
- MIT
Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking the correct BLAST program (blastn/blastp/blastx/tblastn/tblastx/psiblast/megablast/dc-megablast), interpreting Karlin-Altschul E-values, avoiding the max_target_seqs trap (Shah 2019), choosing composition-based statistics, or limiting searches by organism. Covers RID lifecycle, database choice (nt/nr/refseq_select/swissprot), word-size and CBS…
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: BioPython 1.83+, NCBI BLAST+ 2.15+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show biopython` then `help(Bio.Blast.NCBIWWW.qblast)` to check signatures - CLI: `blastn -version` then `blastn -help` If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # BLAST Searches (Remote) **"Find similar sequences in NCBI's database"** -> Submit a query to NCBI's remote BLAST servers; receive a Request ID (RID); poll for completion; parse the XML hit table. Best for one-off identification of a few sequences. For >50 sequences, switch to `local-blast` or DIAMOND/MMseqs2 in `remote-homology`. The two most consequential decisions: **which program** (defines query+target molecule types and word-size defaults) and **which database** (defines the search space and therefore E-value baselines). The third most important: do NOT misuse `max_target_seqs` -- it is an early-termination heuristic, not a "give me the top N hits" filter (Shah et al. 2019). …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-blast-searches@sha256:87f74ebe1aa1eec0The 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_fmiugdjxazke3p64)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_fmiugdjxazke3p64 GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-blast-searches GET https://markdownregistry.com/api/v1/blob/87f74ebe1aa1eec0990d155e73e02913bbecb669a8fac3176d5940ecca7d39ba
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