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

Tue Mar 14 07:58:14 UTC 2006

On 3/13/06, Chris Fields <cjfields at uiuc.edu> wrote:
>
>
> On Mar 13, 2006, at 1:39 AM, neeti somaiya wrote:
>
> 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.
>
>
> This should tell you something here and is likely the source of the
> problem.  Do you have the .ncbirc file set properly?
>
> From BLAST install:
>
> 2) Create a .ncbirc file. In order for Standalone BLAST to operate, you
> have will need to have a .ncbirc file that contains the following lines:
>
> [NCBI]
> Data="path/data/"
>
> Where "path/data/" is the path to the location of the Standalone BLAST
> "data" subdirectory. For Example:
>
> Data=/root/blast/data
>
> The data subdirectory should automatically appear in the directory where
> the downloaded file was extracted. Please note that in many cases it may
> be necessary to delimit the entire path including the machine name and
> or the net work you are located on. Your systems administrator can help
> you if you do not know the entire path to the data subdirectory.
>
> Make sure that your .ncbirc file is either in the directory that you
> call the Standalone BLAST program from or in your root directory.
>
> I believe this can be placed in your home directory though I can't test
> that out.  Are your databases, matrices, etc all in the data directory?
>

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.

What should I do?
>
>
> Don't panic!
>
>
> Any other approach to change the parameters?
> Why is it that e value is taken, but not any other parameter?
>
>
> These are the ones I found in StandAloneBlast, just by looking (hint
> hint):
>
> @BLASTALL_PARAMS = qw( p d i e m o F G E X I q r v b f g Q
>     D a O J M W z K L Y S T l U y Z);
>
> Chris
>
>
>
>
>
> 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
> _______________________________________________
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> Bioperl-l at lists.open-bio.org
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>
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>
>
> --
> -Neeti
> Even my blood says, B positive
>
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>
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>

--
-Neeti
Even my blood says, B positive