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

Chris Fields cjfields at uiuc.edu
Sat Mar 11 20:26:14 EST 2006

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).


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

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