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](https://huggingface.co/spaces/yoshigold/plant-msyn).

To use programmatically:

```python
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