[BioBrew Users] : how to run mpiblast

[Glen Otero]

On Jul 16, 2004, at 8:09 PM, kenix y wrote:

>> formatdb -i ecoli.nt -p F -o T
> breaks up the ecoli.nt into
> ecoli.nt.nhr
> ecolii.nt.nin
> ecolii.nt.nnd
> ecolii.nt.nni
> ecolii.nt.nsd
> ecolii.nt.nsi
> ecolii.nt.nsq
>
> I do not seems to have blast.txt and formatdb.txt in 
> /opt/BioBrew/NCBI/6.1.0/doc.

In BioBrew .9 and 1.0, the docs are probably called:

/opt/BioBrew/NCBI/6.1.0/doc/README.formatdb
/opt/BioBrew/NCBI/6.1.0/doc/README.bls

> I guess I'll have to read on on blast when I have the time, but for 
> now I only need to get to work.

With all due respect, if you don't know how BLAST works, e.g. why '-i 
/path/to/input/file' is mandatory, then you'll *never* get BLAST or 
mpiBLAST to work. BLAST compares an input sequence to a database. 
You're trying to use ecoli.nt as a database, but you have no input 
file?!  What are you interested in comparing to the ecoli.nt database? 
Right now you don't have or understand what a BLAST input sequence is, 
so BLAST will not work, and therefore neither will mpiBLAST. Read up on 
BLAST to understand it some more before you go any further.

>
> Thank you
>
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Glen Otero, Ph.D.
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