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nr- protein database

Hi

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

blast assembly next-gen-sequencing
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updated by Ram Ram • written by Eva_Maria Eva_Maria

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

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written by Farbod Farbod

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.

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updated by Ram Ram • written by gu.fernandezn • gu.fernandezn

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_' ?

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updated by Ram Ram • written by 6schulte • 6schulte

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

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written by raghukiran812 • raghukiran812

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.

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written by GenoMax GenoMax

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.

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written by Sej Modha Sej Modha

1 answer

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
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updated by Ram Ram • written by glihm glihm

Thank you for your reply

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

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updated by Ram Ram • written by Eva_Maria Eva_Maria

Try this:

wget 'ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*.tar.gz'
cat nr.*.tar.gz | tar -zxvi -f - -C .
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updated by Ram Ram • written by Eliad • Eliad

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.

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updated by Ram Ram • written by glihm glihm

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

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updated by Ram Ram • written by snar86 • snar86

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