Databases

We offer various databases suggested by our users that you can access from our S3 storage.

Please bear in mind: The database feature is a functionality that is still under development. An automatic check of the data provided is currently still pending, so we cannot guarantee that the data contained on the links corresponds to that of the specified databases.

You can use Minio Client to download them onto your machine. After installing the Minio Client, you can set an alias to access databases stored at the following locations:

Setting Minio Alias
Bielefeld:
mc alias set denbi https://openstack.cebitec.uni-bielefeld.de:8080 "" ""

alphafold

Version:
Total File Size: 155.63 GB
Total Files: 51
S3 Path:
mc cp --recursive denbi/data/alphafold/v4/databases .

blast_db

Version:
Total File Size: 504.69 GB
Total Files: 8
S3 Path:
mc cp --recursive denbi/data/blast_db/2023-07-31/FASTA .

card

DOI: 10.1093/nar/gkac920
Version:
Total File Size: 3.90 MB
Total Files: 1
S3 Path:
mc cp --recursive denbi/data/card/3.2.7/data .
data 3.90 MB
Download

checkm

DOI: 10.5281/zenodo.7401545
Version:
Total File Size: 288.59 MB
Total Files: 1
S3 Path:
mc cp --recursive denbi/data/checkm/v1 .
content 288.59 MB
Download

checkm2

DOI: 10.5281/zenodo.4626518
Version:
Total File Size: 1.74 GB
Total Files: 1
S3 Path:
mc cp --recursive denbi/data/checkm2/v2 .
content 1.74 GB
Download

gtdb_tk

DOI: 10.1093/bioinformatics/btz848
Version:
Total File Size: 83.34 GB
Total Files: 1
S3 Path:
mc cp --recursive denbi/data/gtdb_tk/2023-06-09/auxiliary_files .
gtdbtk_data.tar.gz 83.34 GB
Download

plsdb

DOI: 10.1093/nar/gky1050
Version:
Total File Size: 3.46 GB
Total Files: 2
S3 Path:
mc cp --recursive denbi/data/plsdb/2021_06_23_v2 .
plasmids_meta.tar.bz2 1.77 GB
Download
plsdb.fna.bz2 1.68 GB
Download

uniref

Version:
Total File Size: 110.40 GB
Total Files: 2
S3 Path:
mc cp --recursive denbi/data/uniref/2023-11-08/uniref90 .
uniref90.xml.gz 66.56 GB
Download
uniref90.fasta.gz 43.85 GB
Download
Setting Minio Alias
Giessen:
mc alias set denbi https://s3.computational.bio.uni-giessen.de "" ""

alphafold

Version:
Total File Size: 155.63 GB
Total Files: 51
S3 Path:
mc cp --recursive denbi/data/alphafold/v4/databases .

blast_db

Version:
Total File Size: 504.69 GB
Total Files: 8
S3 Path:
mc cp --recursive denbi/data/blast_db/2023-07-31/FASTA .

card

DOI: 10.1093/nar/gkac920
Version:
Total File Size: 3.90 MB
Total Files: 1
S3 Path:
mc cp --recursive denbi/data/card/3.2.7/data .
data 3.90 MB
Download

checkm

DOI: 10.5281/zenodo.7401545
Version:
Total File Size: 288.59 MB
Total Files: 1
S3 Path:
mc cp --recursive denbi/data/checkm/v1 .
content 288.59 MB
Download

gtdb_tk

DOI: 10.1093/bioinformatics/btz848
Version:
Total File Size: 83.34 GB
Total Files: 1
S3 Path:
mc cp --recursive denbi/data/gtdb_tk/2023-06-09/auxiliary_files .
gtdbtk_data.tar.gz 83.34 GB
Download

plsdb

DOI: 10.1093/nar/gky1050
Version:
Total File Size: 3.46 GB
Total Files: 2
S3 Path:
mc cp --recursive denbi/data/plsdb/2021_06_23_v2 .
plasmids_meta.tar.bz2 1.77 GB
Download
plsdb.fna.bz2 1.68 GB
Download

uniref

Version:
Total File Size: 110.40 GB
Total Files: 2
S3 Path:
mc cp --recursive denbi/data/uniref/2023-11-08/uniref90 .
uniref90.xml.gz 66.56 GB
Download
uniref90.fasta.gz 43.85 GB
Download
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