nr- protein database

Question

[Eva_Maria]

Hi

I want to download all nr-protein database from ncbi. Is there any link is available for this?

[GouthamAtla]

Either download entire fasta and make your own database ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz or download database which can be downloaded in multiple chunks.

[Farbod]

Hi @geek_y, the FTP that @glihm has provided seems that is an updating FTP that new files are going to add to it after a while. Is the "one-file-format" that you have mentioned above is an updating file or just it is always old? thanks

[gu.fernandezn]

Hi, is there a way to download just a file with the taxonomy information. I mean, a tab delimiter with:

name_of_protein   organism_source(plant, bacteria, other)

I need getting the organism source, but if I take a look for nr db directly have a huge header for each protein and don't exist any pattern a priori to getting that.

[6schulte]

Hi,

I know this question is rather old but maybe someone will be needing this information anyways: Use epost and esummary (NCBIs eutils) to obtain information on the lineage. Something like this could help:

cat "$ListWithAccessionNumbers" | epost -db protein |\
    esummary -db taxonomy -format xml | \
    xtract  -pattern Seq-entry -element Org-ref_taxname, OrgName_lineage, NCBIeaa, Textseq-id_accession \
    > SummaryTable.tsv

You finde more detailed information and suggestions on how and what to execute specifically here: How to get summary for acc.no. not starting with 'WP_' ?

[raghukiran812]

Hi everyone, Where can I download nr.fa file of 2016 which contains gi id's

[GenoMax]

Archival copies of blast databases are not available from NCBI, so there is no easy way to get/recreate a copy of nr database as it existed in 2016. gi numbers have also been deprecated for end-users. Use accession numbers instead.

[Sej Modha]

Please do not post new questions in the answer field, it is reserved for answers only. Using the answer field to post a new question is strongly discouraged, please post a new question with relevant details instead.

Answer 1

[glihm]

Hi there,

You have the FTP site of the NCBI where all databases are available (Url, if the link does not work : ftp://ftp.ncbi.nlm.nih.gov/blast/db/).

Then, in the README, you can find all descriptions of these databases.

For instance:

nr.*tar.gz                    | Non-redundant protein sequences from GenPept, 
                                Swissprot, PIR, PDF, PDB, and NCBI RefSeq

[Eva_Maria]

Thank you for your reply

I want to download all available nr - protein database as a single file

[Eliad]

Try this:

wget 'ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*.tar.gz'
cat nr.*.tar.gz | tar -zxvi -f - -C .

[glihm]

Files size is huge. You can not have one file with all data. The solutions proposed by Eliad allows you to download all "nr" databases subfiles in one command.

[snar86]

Hi, may I know how to format the nr databases subfiles before using for blast?

[gu.fernandezn]

Hi, I found a command to format nr db:

./blast-2.2.18/bin/formatdb -i NR -p T -o T

http://zhanglab.ccmb.med.umich.edu/bbs/?q=node/100 it's an older report. I didn't prove it.