[Bioperl-l] Setting Parameters when Using Remote Blast

Lakshmi Kastury skastu01 at students.poly.edu
Thu Apr 29 00:19:57 EDT 2010







Hi,
I am currently learning Bioperl and need a little help with how to specify parameters when using Remote Blast on a set of protein sequences. I need to have the output sort and display by the highest hsp (lowest e-value) for each sequence.

The previous example I am following specifies each parameter like this:
my $prog = 'blastp';
  my $db   = 'nr';
  my $e_val= '1e-10';
  **my $hit = '682';
  

  my @params = ( '-prog' => $prog,
         '-data' => $db,
         '-expect' => $e_val,
        ** '-hit' => $hit,
         '-readmethod' => 'SearchIO' );

I specified a values at the ** and it gave me an exact match for the sequences. I want it to sort based on the highest score (hsp).

Thanks,
Lakshmi Kastury
 		 	   		  


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