[Bioperl-l] Restriction Analysis

Vidya Oruganti grapevine.256 at gmail.com
Mon Jul 26 00:27:16 EDT 2010


Dear All,

I am interested in knowing if there is a way to perform the restriction
analysis module on many sequences at once. Currently I am retrieving
sequences of contigs one by one from genbank and performing the restriction
analysis individually. This is the script I am using:


  use Bio::Restriction::Analysis;
  use Bio::DB::GenBank;
  use Data::Dumper;


    use Bio::DB::GenBank;
    $gb = Bio::DB::GenBank->new();
    $seq = $gb->get_Seq_by_gi('405830'); # GI Number



  my $ra = Bio::Restriction::Analysis->new(-seq=>$seq);

   print "There are ", scalar $ra->zero_cutters->each_enzyme,
        " enzymes that do not cut\n";

   printf "\n%-10s%s\n", 'Enzyme', 'Number of Cuts';
  my $all_cutters = $ra->cutters;
  map {
      printf "%-10s%s\n", $_->name, $ra->cuts_by_enzyme($_->name)
  } $all_cutters->each_enzyme;

I would like to know whether it would be possible to get an array of
sequences from genbank instead of just one and run the restriction analysis
on all the sequences at one go and get several outputs at once. I have been
able to retrieve more than one sequence from genbank but I'm not able to run
the analysis on more than one sequence.

Thank you


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