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Downloading mmseqs databases !
By Abhi 1143 days ago
# 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 - https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA
- NT Nucleotide - https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA
- 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
- eggNOG Profile - http://eggnog5.embl.de
- dbCAN2 Profile - http://bcb.unl.edu/dbCAN2
- Resfinder Nucleotide - https://cge.cbs.dtu.dk/services/ResFinder
- Kalamari Nucleotide yes https://github.com/lskatz/Kalamari
#For example, run the following to download and setup the Swiss-Prot at the output path outpath/swissprot:
mmseqs databases UniProtKB/Swiss-Prot outpath/swissprot tmp
#In this case, since Swiss-Prot has a value yes in the Taxonomy column above, all necessary files to use it as a valid seqTaxDB will be downloaded and prepared by the databases command.
More information @ https://github.com/soedinglab/mmseqs2/wiki#downloading-databases
