plantiSMASH database#

The plantiSMASH database contains a set of precalculated results for selected species. These are updated every plantiSMASH version. See the Changelog section.

See an overview of results for plantiSMASH 2.0 database:

The full overview of the results is available on the webserver at plantiSMASH 2.0 database.

This directory contains precalculated plantiSMASH database accessible at:
🔗 https://plantismash.bioinformatics.nl/precalc/v2

📁 Directory Structure#

precalc/
├── README.html                  # Overview of plantiSMASH precalculated database (v1–v2)
├── v1/                          # plantiSMASH 1.0 precalculated results
├── v2-beta1/                    # plantiSMASH 2.0 beta 1 results
├── v2-beta4/                    # plantiSMASH 2.0 beta 4 results
└── v2/                          # plantiSMASH 2.0 stable release
    └── tfbs-finder/             # TFBS module results for Arabidopsis thaliana
        ├── README-tfbs-finder.html  # Description of TFBS-finder results and data sources
        ├── Arabidopsis_thaliana_GCF_000001735.4_354PWMs/ # results for 354 manually curated PWMs 
        └── Arabidopsis_thaliana_GCF_000001735.4_576PMWs/ # results for 576 filtered PWMs

Details on plantiSMASH database versioning and status#

Precalc Folder	plantiSMASH version used to generate the output	clusterBLAST Database used	Public Release Date	Nr. of genomes	Notes	Status (Public or Archived)
`v1/`	1.0	clusterBLAST database hosted on GitHub plantiSMASH 1.0 release https://github.com/plantismash/plantismash/releases/tag/1.0	DATE	49	Coexpress module results available in Arabidopsis thaliana https://plantismash.bioinformatics.nl/precalc/v1/Arabidopsis_thaliana/	Public in the plantiSMASH database https://plantismash.bioinformatics.nl/precalc/v1
`v2-beta1/`	2.0 beta 1	clusterBLAST available at 10.5281/zenodo.16927685	DATE	387	NOTES	Public in the plantiSMASH database https://plantismash.bioinformatics.nl/precalc/v2-beta1
`v2-beta4/`	2.0 beta 4	clusterBLAST available at 10.5281/zenodo.17178066	DATE	387	NOTES	Public in the plantiSMASH database https://plantismash.bioinformatics.nl/precalc/v2-beta4
`v2/`	2.0	clusterBLAST available at 10.5281/zenodo.17396002	Public stable release	430	TFBS module results available in Arabidopsis thaliana for 1*10-4 p-value and 500 bp window scanning size.	Public in the plantiSMASH database https://plantismash.bioinformatics.nl/precalc/v2
`v2.0.4`	2.0.4	clusterBLAST available at 10.5281/zenodo.17396002	Submitted: 2025-10-29	430	plantiSMASH-2.0.4 database (with internal cyclopeptide repeat detection only) using the `--require-internal-cyclopeptide-repeats` flag. This is a more restrictive mining method for putative cyclopeptide BGCs, leading to fewer proposed cyclopeptide hits. See Cyclopeptide detection module	Archived at 10.5281/zenodo.17472814

⚙️ Usage#

When running plantiSMASH locally, you can specify the clusterBLAST database path with the corresponding version you wish to reproduce:

run_antismash.py input.gbk --clusterblast --clusterblast-database /path/to/precalc/clusterblastdb/

📄 License and Citation#

See How to cite plantiSMASH.