[Bioperl-l] urgent help required - syntax for using paramatersdifferent from default in standalone blast

[neeti somaiya]

Hi,

I am using blast 2.2.13 on a linux machine.

I tried this:

@params = ('program'  => 'blastn','database' => 'human.rna.fna','e' =>
'0.0001', 'Matrix' => 'BLOSUM80', '_READMETHOD' => 'SearchIO' );

But, this din't help.

I checked the data folder, it has BLOSUM80.

Even a simple blastall command like
blastall -i tryn.fasta -p blastn -d human.rna.fna -o blastoutput -M BLOSUM80
doesnt show BLOSUM80 in the results.

What should I do?

Any other approach to change the parameters?
Why is it that e value is taken, but not any other parameter?







On 3/12/06, Chris Fields <cjfields at uiuc.edu> wrote:
>
> Ah.  I thought that RemoteBlast and StandAloneBlast had similar
> settings.  My bad.  Would be nice to maybe move some of the common
> features to another module that both can inherit from (like parsing/
> saving output, map parameters for each like SearchIO, etc).
>
> Chris
>
> On Mar 11, 2006, at 4:17 PM, Torsten Seemann wrote:
>
> >> Although I believe there is a major reworking
> >> of the Bio::Tools::Run BLAST modules planned
> >
> > Yes there is, but Roger Hall fell ill during our initial
> > discussions so we are
> > a little behind on that one.
> >
> > I'm pretty sure that
> >> everything still works, at least in the latest developer version.
> >> Lots of people are running it so I'm guessing something is wrong with
> >> the logic here otherwise we would have heard about this a while ago.
> >
> > Agreed - at least in the bioperl-live version.
> >
> >> I'm not an expert about this module either but I believe Brian's
> >> right about _READMETHOD.   When using SearchIO directly this is set
> >> using "-readmethod => 'SearchIO'" for text, 'blastxml' for xml, and
> >> 'blasttable' for tabular.
> >
> > Actually, 'blastxml' is NOT supported in bioperl-live version, and
> > it doesn't
> > appear to have ever been supported! It won't be hard to patch in.
> >
> > Also, the current StandAloneBlast does not handle these newer
> > "blastall"
> > parameters (need to add to @BLASTALL_PARAMS)
> >
> >    -R  PSI-TBLASTN checkpoint file [File In]  Optional
> >    -n  MegaBlast search [T/F]
> >    -L  Location on query sequence [String]  Optional
> >    -A  Multiple Hits window size, default if zero (blastn/megablast
> > 0, all
> > others 40 [Integer]
> >    -w  Frame shift penalty (OOF algorithm for blastx) [Integer]
> >    -t  Length of the largest intron allowed in a translated
> > nucleotide sequence
> > when linking multiple distinct alignments. (0 invokes default
> > behavior; a
> > negative value disables linking.) [Integer]
> >    -B  Number of concatenated queries, for blastn and tblastn
> > [Integer]  Optional
> >    -V  Force use of old engine [T/F]  Optional
> >    -C  Use composition-based statistics for tblastn:
> >    -s  Compute locally optimal Smith-Waterman alignments (This
> > option is only
> >
> > According to the POD for StandAloneBlast
> >> SearchIO::blast is default;  have you tried not using that flag
> >> (removing it)?
> >
> > Yes, _READMETHOD='BLAST' (which uses Bio::SearchIO for parsing) is
> > the default,
> > and does not need to be set in Neeti's examples.
> >
> > --
> > Torsten Seemann
> > Victorian Bioinformatics Consortium, Monash University, Australia
> > http://www.vicbioinformatics.com/
> > Phone: +61 3 9905 9010
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>


--
-Neeti
Even my blood says, B positive