Question: What is the Non Redundant NCBI database NAME?
0
gravatar for soza
2.6 years ago by
soza10
soza10 wrote:

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

blast ncbi • 1.5k views
ADD COMMENTlink modified 2.6 years ago by Farbod3.2k • written 2.6 years ago by soza10

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.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Jenez520
0
gravatar for 5heikki
2.6 years ago by
5heikki8.4k
Finland
5heikki8.4k wrote:

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

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

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by 5heikki8.4k
0
gravatar for Farbod
2.6 years ago by
Farbod3.2k
Toronto
Farbod3.2k wrote:

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

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Farbod3.2k
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