Where can I find prebuilt diamond databases that also contain taxonomy information?
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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?

taxonomy database diamond alignment protein • 1.2k views
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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.

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