Entering edit mode
2.8 years ago
O.rka
▴
740
I found this but I think it's specifically for UPPSALA UNIVERSITY: https://www.uppmax.uu.se/resources/databases/diamond-protein-alignment-databases/
MMSeqs2 has prebuilt databases: https://github.com/soedinglab/mmseqs2/wiki#downloading-databases
# mmseqs databases
Usage: mmseqs databases <name> <o:sequenceDB> <tmpDir> [options]
Name Type Taxonomy Url
- UniRef100 Aminoacid yes https://www.uniprot.org/help/uniref
- UniRef90 Aminoacid yes https://www.uniprot.org/help/uniref
- UniRef50 Aminoacid yes https://www.uniprot.org/help/uniref
- UniProtKB Aminoacid yes https://www.uniprot.org/help/uniprotkb
- UniProtKB/TrEMBL Aminoacid yes https://www.uniprot.org/help/uniprotkb
- UniProtKB/Swiss-Prot Aminoacid yes https://uniprot.org
- NR Aminoacid yes https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA
- NT Nucleotide - https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA
- GTDB Aminoacid yes https://gtdb.ecogenomic.org
- PDB Aminoacid - https://www.rcsb.org
- PDB70 Profile - https://github.com/soedinglab/hh-suite
- Pfam-A.full Profile - https://pfam.xfam.org
- Pfam-A.seed Profile - https://pfam.xfam.org
- Pfam-B Profile - https://xfam.wordpress.com/2020/06/30/a-new-pfam-b-is-released
- CDD Profile - https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
- eggNOG Profile - http://eggnog5.embl.de
- VOGDB Profile - https://vogdb.org
- dbCAN2 Profile - http://bcb.unl.edu/dbCAN2
- SILVA Nucleotide yes https://www.arb-silva.de
- Resfinder Nucleotide - https://cge.cbs.dtu.dk/services/ResFinder
- Kalamari Nucleotide yes https://github.com/lskatz/Kalamari
That can be downloaded via: mmseqs databases UniProtKB/Swiss-Prot outpath/swissprot tmp
Is there any similar resource with Diamond?
Latest version of DIAMOND can use NCBI's pre-formatted databases. I assume that will include taxonomy information as well if you download taxdb data files.