Is it possible to download nr db from NCBI's cloud ?

Question

[K.Gee]

Hello everyone. Im trying to install nr db locally.

I found this link in which I can download the entire NR fasta in gz format (ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz) in this case the last modification was on 12/14/19. I also found that in the cloud "ftp://ftp.ncbi.nlm.nih.gov/blast/db/cloud/2020-01-08/ " there are so nr db files which look to be ,more up to date.

Is it any way to download all the .nr,XX files at once?

Answer 1

[GenoMax]

Database files available on NCBI's FTP site are always current. You don't want to download the fasta file for nr since it will take a long time to index nr locally.

NCBI is now making v5 of the databases available here. As you can see they have current time stamps.

You can use update_blastdb.pl or a similarly named script that is included in blast+ package to download all files for a particular (or all) database automatically.

[K.Gee]

Thanks for the response. My problem is that im not so familiar with informatics, so I was thinking of making it manually like downloading the fasta.file and then using makeblastdb to "Installing " the current version of the nrdb locally. I will try to use upade_blastdb.pl instead. Because I am afraid of messing all my files If I type update_blastdb.pl nr --decompress is it going to "substitute" the current db files with the current ones?

[GenoMax]

If you already have a copy of the nr database then it will be updated with the current version (script only downloads changed files to avoid having to download entire dataset). No other database files should be touched than the one you are trying to update.

If you don't wish to do that then you may want to download the entire dataset in a different directly. See in-line help for the update script for more info.

[K.Gee]

ok i see. Thank you very much once again!