Entire genome databases can be downloaded from our FTP site.
Please be aware that some of these files can run to many gigabytes of data.
Each directory on our FTP site contains a README file, explaining the directory structure or data format.
Read genome assembly and annotation detail.
| Version | Genome | CDS | Protein | Annotation | Variation |
|---|---|---|---|---|---|
| Version-2019 | FASTA (Genome) |
FASTA (CDS) |
FASTA (Protein) |
GFF (Annotation) |
VCF (Variation) |
| Version-2021 | FASTA (Genome) |
FASTA (CDS) |
FASTA (Protein) |
GFF (Annotation) |
| FASTA | FASTA sequence for genome and predicted genes and proteins. Since the FASTA format does not permit sequence annotation, these files are mainly intended for use with local sequence similarity search algorithms. Each directory has a README file with a detailed description of the files and their header line format. | |
|---|---|---|
| Genome | Assembled genome sequence file. Whole-genome sequence and the sequence of each chromosome are accessible. | |
| CDS | Coding sequences for ab initio predicted genes. | |
| Protein | Protein sequences for ab initio predicted genes. | |
| GFF | GFF (Gene Feature Format) format annotation file. GinkgoDB provides an automatic gene annotation for Ginkgo biloba using protein sequences from five land plants coupled with transcriptomes assembled from RNA-seq data and EST data downloaded from NCBI. For more information see the README files in the annotation directory. | |
| VCF | VCF (Variant Call Format) format file for variation positions across the Ginkgo biloba genome. For more information see the README files in the variation directory. | |
Researchers who wish to use GinkgoDB are encouraged to refer to our publication or specific data sources :
Kai-Jie Gu, Chen-Feng Lin, Jun-Jie Wu, Yun-Peng Zhao* (2022) GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba. Database 2022, baac046
doi: 10.1093/database/baac046