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Datasets:
Yoshigold
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plant-msyn-data

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Other
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1B<n<10B
Tags:
biology
genomics
synteny
plants
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plant-msyn-data
File size: 2,410 Bytes
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---
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