bio-comparative-genomics-synteny-analysis SKILL.md skillA
bio-comparative-genomics-synteny-analysis 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-comparative-genomics-synteny-analysis@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
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- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-comparative-genomics-synteny-analysis/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
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- License
- MIT
Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting…
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: MCScanX 1.0+ (wyp1125/MCScanX commit 2020+), JCVI 1.4.21+ (Python port of MCScan), GENESPACE 1.4.0+ (Lovell 2022 eLife 11:e78526), SyRI 1.7.1+ (Goel 2019 Genome Biol 20:277), plotsr 1.1.1+, AnchorWave 1.2.5+ (Song 2022 PNAS 119:e2113075119), i-ADHoRe 3.0.01+, SynNet (Zhao 2017 Plant Cell 29:1278), ntSynt 1.0.4+ (2024), minimap2 2.28+, MUMmer 4.0.0+, OrthoFinder 3.0+, R 4.4+. plotsr requires pysam 0.22+ and seaborn 0.13+.
Before using code patterns, verify installed versions match. If versions differ:
- CLI: `MCScanX -h`; `syri --version`; `python3 -m jcvi.compara.catalog ortholog --help`
- R: `packageVersion('GENESPACE')`; `?run_genespace`
- Python: `pip show jcvi`
If code throws `MCScanX: argument bad format`, `syri: input alignment file missing required columns`, or `GENESPACE: GFF parse error`, these tools have brittle input parsing: MCScanX requires 4-column `species_chr gene start end` BED (non-standard), JCVI expects 4-column simple BED, GENESPACE requires GFF3 with `gene` feature type. Pre-process with `jcvi.formats.gff bed` or custom AWK.
# Synteny Analysis
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-comparative-genomics-synteny-analysis@sha256:2e6336d61094a3ddThe 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_wbd65ctqvrllx2na)
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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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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_wbd65ctqvrllx2na GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-comparative-genomics-synteny-analysis GET https://markdownregistry.com/api/v1/blob/2e6336d61094a3dd68bb695a14a5d48d439b5916eb6b254390c13bb6ae596878
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