[Bioperl-l] about blast

Dimitar Kenanov dimitark at bii.a-star.edu.sg
Mon Jun 7 22:02:31 EDT 2010

Hi guys,
i stumbled upon a problem.

How can i run a psiblast with StandAloneBlastPlus without the query? I 
mean in normal psiblast there is a possibility that one can actually 
blast with the option '-in_pssm' instead of query. Of course first you 
need to run a psiblast with more than one iterations with option 
'-out_pssm' which produces the file which can be used by '-in_pssm'.

Now in BioPerl i removed my query from the options and i got:
MSG: Blast run: query data required, use -query
STACK: Error::throw
STACK: Bio::Root::Root::throw 
STACK: Bio::Tools::Run::StandAloneBlastPlus::run 

Somehow it would be nice to check the method args in the module and when 
there is the option '-in_pssm' the check for query should be 
different(opposite to the one now).

I hope i made it clear :)


Dimitar Kenanov
Postdoctoral research fellow
Protein Sequence Analysis Group
Bioinformatics Institute
A*STAR, Singapore
tel: +65 6478 8514

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