[Bioperl-l] How to run blastn with -task blastn option from Bio::Tools::Run::StandAloneBlastPlus?

Peng Yu pengyu.ut at gmail.com
Tue Jun 8 21:00:07 EDT 2010


I need to use Bio::Tools::Run::StandAloneBlastPlus to run the following command.

blastn -task blastn -query first.fa -subject second.fa

I tried the following code, which works like without the '-task
blastn' option. Would you please let me know how to supply the option
in Bio::Tools::Run::StandAloneBlastPlus?

my $factory = Bio::Tools::Run::StandAloneBlastPlus->new();
  my $result=$factory->bl2seq(
    -query=> $seq1,
    -subject=> $seq2

Thank you for you help!


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