Download all Becteria and protist fasta protein sequences from UNIPROT proteomes
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This help page on the UniProt website https://www.uniprot.org/help/api_downloading includes a code example to "Download the UniProt reference proteomes for all organisms below a given taxonomy node in compressed FASTA format"
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Elisabeth Gasteiger
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Hello, I downloaded the file : https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_sprot_bacteria.dat.gz and transform the .dat into .fasta using the python function Bio.SwissProt but I only get 335 066 fasta bacterial sequence despti the fact that when I type on uniprot :
taxonomy:bacteriain the research tab I up to 151,792,141 bacterial sequence. Do you know why?You have a better solution provided by Elisabeth Gasteiger below.
You can use
seqretfrom EMBOSS to convert thedatfiles to fasta. I am not sure why you get a smaller number of entries. Perhaps redundant sequences are represented only once.Ok I see, in fact I only download the swissprot part and not the Trembl part, I will check if the number of entries is good from that.