What is the Non Redundant NCBI database NAME?

Question

[soza]

Hey guys, I want to run a remote blast on non-redundant database from NCBI but I dont know the name, does anyone here know what is?

example:

blastn -db rRNA_typestrains/prokaryotic_16S_ribosomal_RNA -query inputfile.fasta -out outputfile.xml -remote -max_target_seqs 3 -outfmt 5

blastn -db (nonreduntantHERE) -query inputfile.fasta -out outputfile.xml -remote -max_target_seqs 3 -outfmt 5

I tried nr/nt without sucess

thank you for your time

[Jenez]

What do you mean by without success? Do you get an error message? What does it say? Did nothing happen? Details plix plox!

blastn -db nt -query inputfile.fasta -out outputfile.xml -remote -max_target_seqs 3 -outfmt 5

Worked fine for me btw.

Answer 1

[5heikki]

It's called just "nt". The protein "equivalent" is "nr".

See ftp://ftp.ncbi.nlm.nih.gov/blast/db/README

Answer 2

[Farbod]

Dear Soza, Hi.

non-redundant NCBI database (that you have mentioned it in your post title) is usually referred to it's nr protein database which you can find in this ftp (e.g. nr.00.tar.gz).

By the way, if you intend to search your nucleotide query against it, you should use blastX

In addition to NCBI, there are other non-redundant database, too.

~ Best