Download all RefSeq proteins from all organisms in one faa-file

Question

[seth97]

How can I download all RefSeq proteins from all organisms in one faa-file?

I'm looking at NCBI RefSeq FTP: ftp://ftp.ncbi.nlm.nih.gov/refseq/

I can for example get the rat RefSeq: ftp://ftp.ncbi.nlm.nih.gov/refseq/R_norvegicus/mRNA_Prot/rat.1.protein.faa.gz

But how can I get all organisms in one file?

Sorry if this is an obvious question.

Thanks!

[seth97]

Thanks for that!

For combining the files I did these commands in the Terminal (mac):

find ./ -name \*.gz -exec gunzip -k {} \;
cat *.faa > ~/output.txt

[unksci]

If you were not restricted to RefSeq, you could download such a single faa directly from Uniprot: http://www.uniprot.org/downloads .

Answer 1

[Pierre Lindenbaum]

Use wget to download everything under ftp://ftp.ncbi.nlm.nih.gov/refseq/release// (http://serverfault.com/questions/25199) and using option --accept=LIST to only keep *.faa.gz , and then concatenate the fasta files....

[5heikki]

Wouldn't this suffice?

wget ftp://ftp.ncbi.nlm.nih.gov/refseq/release/complete/*.faa.gz

From: ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-notes/RefSeq-release69.txt

The data that comprises a RefSeq release are available in several file formats, as indicated by the format component in the file name:
bna binary ASN.1 format; includes nucleotide and protein
gbff GenBank flat file format; nucleotide records
gpff GenPept flat file format; protein records
fna FASTA format; nucleotide records
faa FASTA format; protein records

The comprehensive full release is deposited in the "complete" directory and is available in all file types.

[Pierre Lindenbaum]

Most probably