<p>Hello all,</p>

<p>I am in a fix. For my work, I need an exhaustive and up-to-date database of<br />
all protein sequences, especially covering ALL eukaryotes sequenced till date.<br />
Thus, I downloaded the latest version of nr database from ncbi&#39;s ftp site.<br />
However, I find that it does not contain all the putative protein<br />
sequences as listed in individual genome databases.</p>

<p>For discussion purposes, let us consider Cyanophora paradoxa (taxonomic<br />
id: 2762). According to the website<br />
<a href="http://cyanophora.rutgers.edu/cyanophora/blast.php" target="_blank">http://cyanophora.rutgers.edu/cyanophora/blast.php</a>, it has 32,167 protein<br />
coding sequences. However, there are only 731 gi ids corresponding to this<br />
species in the latest nr database (25May2014 version). The Cyanophora<br />
paradoxa&#39;s complete genome was published in 2012 (Price DC et al, 2012).</p>

<p>Thus, to me the only option seems to be to download protein sequences from individual genome projects and combining identical entries in one entry. Finally I shall append them to nr database to get the exhaustive set of proteins. However before I begin on this mammoth task, I thought to enquire if there is simpler solution to this problem.</p>

<p>Any help or suggestions are greatly welcomed.</p>

<p>Thanks a lot for your time,<br />
Ramya</p>

Well the current NCBI nr contains 40,337,612 sequences originating from: <a href="http://www.ncbi.nlm.nih.gov/genbank/">GenBank</a> CDS translations (excluding those from environmental samples and WGS projects), <a href="http://www.uniprot.org/help/uniprotkb">UniProtKB/SwissProt</a>, <a href="http://www.pdb.org/">PDB</a> and <a href="http://www.prf.or.jp/">PRF</a>.

UniProt's <a href="http://www.uniprot.org/help/uniparc">UniParc</a> database has more coverage, currently containing 63,875,797 unique protein sequences, including the CDS translations from the <a href="http://www.insdc.org/">INSDC</a> databases (DDBJ, EMBL-Bank and GenBank) which are excluded from NCBI nr, and additional sequences from various other sources.

You could also try having a look at <a href="http://liferay.csb.univie.ac.at/portal/web/simap">SIMAP</a>, this contains additional protein sequences from meta-genomics experiments.

However looking at the paper (<a href="http://europepmc.org/abstract/MED/22344442/">Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants</a>) and searching the nucleotide databases it appears that the only submission has been to the Sequence Read Archive:

 - http://www.ncbi.nlm.nih.gov/Traces/sra/?study=SRP009206
 - http://www.ebi.ac.uk/ena/data/view/SRP009206&display=html

The corresponding assembly and associated feature annotations do not appear to have been submitted as yet, presumably due to this currently being a draft genome. Thus the protein sequences which are derived through translation of INSDC CDS features do not appear in NCBI nr or UniProtKB.

In general you should be able to start from a non-identical sequence archive such as UniParc and add unique protein sequences from other sources, assuming you can obtain them with appropriate annotations for your purposes.