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

[Torsten Seemann]

Chris Fields wrote:
> What version of bioperl are you using?  What OS?  Always a good idea  
> to give these details.  

Neeti, please let us also know the version of "blastall" you are running.
eg. NCBI 2.2.13 ?

> 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