List of NCBI database names for standalone BLAST remote search

Question

[matthewur]

Hello,

I am trying to figure out where/how I can get a list of database names for use with the -remote command for NCBI standalone BLAST (i.e. -db [?]). I searched for this topic in the forum and found only one post, and the page that the answer links to no longer exists. Specifically, I want to know the name of the NCBI 16S Microbial rRNA database. Can anyone help me out here? Thanks in advance.

[bryesk]

It may be a little late for you, but I ran across the same problem today. I found the name of the database is rRNA_typestrains/prokaryotic_16S_ribosomal_RNA. I ran a test on standalone blast like below, which worked fine.

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

[matthewur]

Yes, that works! Thanks so much!

[eem0306]

Is there any way to find other NCBI database lists like prokaryotic refseq genomes? I tried to find "blastdb.txt" file in NCBI ftp but I couldn't. How did you know the name of specific database?

Answer 1

[h.mon]

Look here. Apparently it has the very apt name "16SMicrobial".

[matthewur]

Thanks, but that's actually the first thing I tried. Doesn't work. Here's the command line and error message I get:

blastn -query C:\PostDoc\TRiFLe\Human_mic
robiome_16S_sequences\human_microbiome_sampling.fasta -db "16SMicrobial" -out C:\PhD\VBA_tools\RunStdAloneBLAST\human_microbiome_sampling.xls -outfmt "6 sacc sgi pident evalue" -max_target_seqs 1 -remote

BLAST Database error: '16SMicrobial' not found on NCBI servers.