https://bioinformaticsonline.com/snippets/view/43438/downloading-mmseqs-databases? https://bioinformaticsonline.com/snippets/view/43438/downloading-mmseqs-databases Wed, 06 Oct 2021 06:25:12 -0500 https://bioinformaticsonline.com/snippets/view/43438/downloading-mmseqs-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 - 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]]> Abhi