NCBI nr database

Question

[agata88]

Hi all!

I am looking for explanation about the NCBI nr database which can be selected in PrimerBlast analysis. I found that this is non-redundant database, but what exactly does it include?

Thanks in advance!

Best,

Agata

[GenoMax]

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

[agata88]

Thank you :) Best, Agata

Answer 1

[Hajk-Georg Drost]

In case you wish to download the NCBI nr or NCBI nt (for nucleotide sequences) databases to your hard drive with the R programming language you can use the biomartr package.

Simply type:

# download the entire NCBI nr database
biomartr::download.database.all(db = "nr")

or

# download the entire NCBI nt database
biomartr::download.database.all(db = "nt")

In case you wish to see all available databases:

# these NCBI databases can be downloaded
biomartr::listDatabases(db = "all")

Please note that when downloading the NCBI nr or nt database the entire database is chopped up into smaller data packages to make the download more reliable.

For more detailed information you can consult the Database Retrieval vignette.

I hope this helps.