Datasets:

Yoshigold
/

plant-msyn-data

license: mit
task_categories:
  - other
tags:
  - biology
  - genomics
  - synteny
  - plants
pretty_name: Plant Microsynteny Data
size_categories:
  - 1B<n<10B

Plant Microsynteny Dataset (plant-msyn-data)

Pre-computed MCscan protein-based synteny analysis results for 30+ plant genomes.

Dataset Structure

plant-msyn-data/
├── mcscan_results/
│   ├── bed_files/           # Gene position files (*.bed) + database_genomes.txt whitelist
│   ├── i1_blocks/           # Synteny block files (*.i1.blocks)
│   ├── lifted_anchors/      # Syntenic anchor pair files (*.lifted.anchors)
│   ├── last_filtered_by_i1/ # I1-filtered LAST alignments
│   ├── pep_files/           # Protein FASTA files (*.pep)
│   ├── custom_meta/         # Custom genome metadata (user uploads)
│   └── custom_synteny_meta/ # Custom synteny project metadata
├── sql/
│   ├── search_catalogs/     # Per-genome SQLite catalogs for fast gene lookups
│   └── plantmsyn_metadata.db # Central metadata database
└── annotations/
    └── [species_name]/
        └── gene_annotation.tsv  # Gene functional descriptions

Supported Genomes

The dataset includes synteny data for 30+ plant genomes including:

Barley (Hordeum vulgare)
Wheat (Triticum aestivum)
Rice (Oryza sativa)
Maize (Zea mays)
Arabidopsis (Arabidopsis thaliana)
And 25+ more species

Usage

This dataset is designed to be used with the Plant-mSyn web application.

To use programmatically:

from huggingface_hub import snapshot_download

# Download the full dataset
local_path = snapshot_download(
    repo_id="yoshigold/plant-msyn-data",
    repo_type="dataset"
)

File Formats

BED Files (`*.bed`)

Tab-separated files with gene positions:

Column 1: Chromosome
Column 2: Start position
Column 3: End position
Column 4: Gene ID
Column 5: Score
Column 6: Strand

Blocks Files (`*.i1.blocks`)

Tab-separated synteny block definitions linking genes between species.

Annotation Files (`gene_annotation.tsv`)

Tab-separated files with:

Column 1: gene (Gene ID)
Column 2: description (Functional annotation)

Citation

If you use this dataset, please cite:

MCscan/JCVI: Tang et al. (2008) Synteny and Collinearity in Plant Genomes