bioperl problem

subhomoi.bk has asked for the wisdom of the Perl Monks concerning the following question:

i m new to bioperl..plz help me on this..when i used the following code...an error msg comes "Target sequence not defined"..so where is $bio_seq? i want to design a siRNA prediction tool

use Bio::Tools::SiRNA;

     

  my $sirna_designer = Bio::Tools::SiRNA->new( -target => $bio_seq,
                                               -rules  => 'tuschl'
    );

<p> where should i put the target sequence</p>
  my @pairs = $sirna_designer->design;


  foreach $pair (@pairs)

 {
      my $sense_oligo_sequence = $pair->sense->seq;
      my $antisense_oligo_sequence = $pair->antisense->seq;

     
      print join ("\t", $pair->start, $pair->end, $pair->rank,
                  $sense_oligo_sequence, $antisense_oligo_sequence), "
+\n";
  }
[download]

Comment on bioperl problem Download Code

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Re: bioperl problem by vivekkrish (Initiate) on Jun 03, 2011 at 20:38 UTC
Comment made by 'Anonymous Monk' is incorrect. $bio_seq is infact a Bio::Seq::RichSeq object This object is an input sequence from a rich sequence database such as GenBank, SwissProt and EMBL. You can create such an object using the following code snippet (code pulled from cpan docs): `$seq = Bio::Seq::RichSeq->new( -seq => 'ATGGGGGTGGTGGTACCCT', -id => 'human_id', -accession_number => 'AL000012', );` [download] There is documentation available for Bio::Tools::SiRNA here Hope this is useful!!	[reply] [d/l]
Re: bioperl problem by Anonymous Monk on Jun 03, 2011 at 20:13 UTC
In your snippet of code, $bio_seq is a Bio::SeqIO object pointing to an output FASTA file You can create such an object like so: `use strict; use warnings; use Bio::SeqIO; my $bio_seq = Bio::SeqIO->new( -file => '>outputfilename', -format => 'Fasta' );` [download] where: 'outputfilename' is the name of your desired output file. Friendly reminder: always remember to use the 'strict' pragma and enable 'warnings' to make sure you can identify problem areas in your code.	[reply] [d/l]