[Bio-Linux] (no subject)

[Tim Booth]

Hi Roy,

If you want to run a BLAST search without downloading the database you
can use the -remote flag, so:

blastp -query PROTEIN_SEQ.fa -db nr -out PROTEIN_SEQ.blast -remote

But because this uses the processing power on the NCBI servers it will
potentially be a lot slower than downloading the database for yourself,
so if you are processing a whole lot of sequences you should probably
download the database files from FTP first.

Cheers,

TIM

On Sat, 2015-04-25 at 18:53 +0100, Roy Lee wrote:
> 
> > >
> > >My name is Roy Lee. With Hunter College in New York city.
> > >When I am running a blast search from the command line for a
> protein fasta
> > >file, I keep getting asked where the nr reference database is. May
> you please
> > >let me know what I need to do to access that database on my blast
> search? I
> > >don\'t think I should be downloading a 15GB database onto my ubuntu
> VM.
> > >
> > >I\'m in the ubuntu terminal  , so far, I\'ve written
> > >
> > >$ blastp -query PROTEIN SEQ.fa -db $blastdb/nr -out PROTEIN
> SEQ.blast
> > >
> > >
> > >I keep getting the error message that the nr database is
> non-existent. Would
> > >you happen to know where this database is? Thanks.
> > >Thanks for your help.
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

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