[BiO BB] megablast and blastp index errors

[Martin Gollery]

No problem.
Yes, you can run multiple entries at a time with the comand line, but with
the newest version it does not run them one at a time, as the old version
did, but all at once. Then it parses out the results later. This means that
it is much faster- ten times faster, in some cases because the database only
has to be loaded once.

Marty

On 8/31/06, rich <rich at thevillas.eclipse.co.uk> wrote:
>
>
> Ha! Of course, thanks. I just assumed.
> As an aside, taking the same input file I wanted to use for megablast
> (one file with multiple a number of fasta entries) and running
> blastall -p blastp
> seems to work in a similar manner as megablast ie taking one entry at a
> time and blasting against the db. I didn't realise blastall would take
> multiple entries as input
>
> cheers
> Rich
>
> Martin Gollery wrote:
> > astral100 is a protein database- Megablast is only for nucleotides,
> > and so it is looking for astral100.nin which is not there.
> >
> > Marty Gollery
> >
> > On 8/30/06, * rich* <rich at thevillas.eclipse.co.uk
> > <mailto:rich at thevillas.eclipse.co.uk>> wrote:
> >
> >     Hi,
> >
> >     I created a blastable db with formatdb (2.2.10):
> >
> >     formatdb -i astral100
> >
> >     I can run blastall -p blastp and it works fine
> >     but when I run megablast I get
> >
> >     [megablast] WARNING: Could not find index files for database
> >     astral100
> >
> >     Any ideas?
> >     Thanks
> >     Rich
> >     _______________________________________________
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> >
> >
> >
> > --
> > --
> > Martin Gollery
> > Associate Director
> > Center For Bioinformatics
> > University of Nevada at Reno
> > Dept. of Biochemistry / MS330
> > 775-784-7042
> > -----------
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
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>
>


-- 
-- 
Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
775-784-7042
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