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

Chris Fields cjfields at uiuc.edu
Tue Mar 14 09:52:21 EST 2006

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

Okay.  Something I completely missed here since I assumed you knew what you
were doing.  There is a serious error in your logic here.  Why do you need
an AMINO ACID substitution matrix like BLOSUM80 for a NUCLEOTIDE database
search?  You're using BLASTN!  

And, again, you are using _READMETHOD where you don't need it.  The parser
is set to SearchIO by default.  Remove it.


> > 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.

That's right, it won't. I get this:

Matrix: blastn matrix:1 -3

Again, this should tell you something.  The problem here is NOT
StandAloneBlast but your logic. 

> the .ncbirc file is thr and all is properly set in it.
> blast runs with the default and with changed e value, only the problem is
> with changed matrix and gap opening and extension parameters.
You aren't setting the gap opening penalty OR extension parameters in the
parameter list you gave above.  If you're referring to your earlier
correspondence, the following is from the latest release (2.2.13), which
could explain a lot:

Megablast, blastall and bl2seq have until now allowed users to select
arbitrary gap existence and extension penalties for a blastn type
search. This has been convenient for users but has led to the
unfortunate situation that searches with some parameter sets were
significantly overestimating the statistical significance of matches. To
address this problem the proper statistical parameters for a number of
reward/penalty/gap existence/gap extension values have been calculated.

The parameters that might cause an issue here are -r (match reward), -q
(mismatch penalty), -G (gap existence cost), and -E (gap extension
cost). If you do not change these, then nothing will change for you.

> What should I do?
> >
> >
> > Don't panic!

This was not a joke.  Think about what you are trying to do logically.  If
you have problems getting a result using command line args (not using
Bioperl), why would you expect it to work with Bioperl?  

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

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