[Bioperl-l] StandAloneBlast.pm and RemoteBlast.pm

jwon at ucalgary.ca jwon at ucalgary.ca
Thu Jul 22 16:07:35 EDT 2004


I am trying to use StandAloneBlast.pm and RemoteBlast.pm to automate BLASTing 
of several sequences that I am interested in.  I need to use the 'tblastn' 
program against the 'est' database.  However, when i set the parameters for 
the StandAloneBlast.pm and RemoteBlast.pm, I code:

my @params = ('program'=>'tblastn', 'database'=>'est', _READMETHOD=>"Blast")
my $f = Bio::Tools::Run::StandAloneBlast->new(@params);
my $blast_report = $f->blastall($sequence);

but after execution, it tells me:

[blastall] WARNING: gi|11499797|ref|NP_071040.1|: Could not find index files 
for database /a1000/formatted_dbs/genbanknr/est
------------- EXCEPTION --------------
MSG: blastall call crashed: 

when i run the same program with the database parameter set to "swissprot, 
and program set to "blastp", the program works fine.

Do these objects not work with the tblastn program against the est database?

Thank you in advance for your help.


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