<p>Hello,</p>

<p>I&#39;d like to study how NCBI&#39;s non-redundant protein database (nr) has developed over the years. However, I&#39;m yet to find a way to download anything but the latest release from the NCBI ftp. Are those old versions lost for good from the public domain?</p>

As far as I am aware NCBI do not provide archived versions of the 'nr' database, although they might be available upon request.

However since most of the sequences in 'nr' come from the protein translations in GenBank and UniProt provide archived releases for UniProtKB (which includes translations from EMBL-Bank), the UniProt releases would probably cover what you need. See ftp://ftp.uniprot.org/pub/databases/uniprot/previous_releases/.

Alternativly the UniProt's <a href="http://www.uniprot.org/help/uniparc/">UniParc database</a> is equivalent to the NCBI's 'nr' database, and provides additonal date information which would allow you to create subsets based on the database at a particular date. For the XML version of the UniParc database, which contains the additional information, see ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/uniparc/

Please note: the NCBI 'nr' database and the UniParc database are sets of non-identical sequences (i.e. the database contain one sequence for each unique sequence, with meta-data providing details of all the source entries containing the sequence). Non-redundant sequence databases such as <a href="http://www.uniprot.org/help/uniref">UniRef</a> or those generated with <a href="http://cd-hit.org/">CD-HIT</a> are different, and merge subsequences such as those from sequencing fragments into either the longest or a representitive sequence. To generate your own 'nr' like database(s) use the 'nrdb' program (http://blast.advbiocomp.com/pub/nrdb/) on your collection of sequences.