Databases

Franklin's MMG and MCB stakeholders have kindly donated 10TB of storage space for centralized databases. The root databases directory is /share/databases.

alphafold2¶

The core alphafold2 databases are in the alphafold subdirectory, including uniref30, uniref90, uniprot, mgnify, all relevant pdb databases, and alphafold's models. The provided alphafold wrapper script sets these locations automatically.

CryoEM¶

Databases for relion and related tools like deepemhancer are available as well. These locations are automatically configured by the relion modules.

NCBI Blast¶

The blast subdirectory has the following NCBI databases available in blast format:

nr
16S_ribosomal_RNA
18S_fungal_sequences
28S_fungal_sequences
mito
nt_prok
nt_viruses
pdbaa
pdbnt
refseq_protein
swissprot
taxdb

These are updated weekly via NCBI's update_blastdb.pl script.

Please file a ticket to request additional databases.