Downloads

Protein sequences, CDS, BED annotations and collinearity files for all PGDD genomes.

… genomes … with PEP … with CDS … with BED

Visualize in SynVisio Browse Genomes

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Total Genomes

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Protein (PEP)

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CDS Sequences

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BED / GFF

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Gene Type

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Genome Files

… genomes

Species	Abbr	PEP Protein	CDS Sequences	BED Annotation	GT Gene Type
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Collinearity & GFF Downloads

Select two species to download pre-computed collinearity blocks or the combined GFF annotation file for that pair.

Query Species

Target Species

File formats

PEP — Protein FASTA (longest isoform per gene, prefixed with species abbreviation)
CDS — Coding sequences in FASTA format
BED — 4-column MCScanX-compatible genome annotation
Gene Type — Duplication classification per gene
Collinearity — MCScanX synteny blocks for a species pair

Bulk Download via Command Line

Use wget or curl. Replace ABBR with the species abbreviation (e.g. Ath, Bol).

# Download a single genome file
wget "https://chibba.agtec.uga.edu/genome/ABBR/download/pep" -O ABBR.pep
wget "https://chibba.agtec.uga.edu/genome/ABBR/download/cds" -O ABBR.cds
wget "https://chibba.agtec.uga.edu/genome/ABBR/download/bed" -O ABBR.bed

# Collinearity for a species pair
wget "https://chibba.agtec.uga.edu/download/collinearity?query=Ath&target=Bol" -O Ath_Bol.collinearity

# Batch download (bash loop)
for sp in Ath Bol Bra Osa Zma; do
wget -q "https://chibba.agtec.uga.edu/genome/$sp/download/pep" -O ${sp}.pep
wget -q "https://chibba.agtec.uga.edu/genome/$sp/download/cds" -O ${sp}.cds
done

Rate limit: Please keep bulk downloads to ≤ 10 files at a time. Not all genomes have every file type.