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
2 answers
It's called just "nt". The protein "equivalent" is "nr".
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
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What do you mean by without success? Do you get an error message? What does it say? Did nothing happen? Details plix plox!
Worked fine for me btw.