Bio::Seq::PrimedSeq A representation of a sequence and two primers flanking a target region
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Bio::Seq::PrimedSeq Tags

Perl module perl bio target region primed sequence primed

Bio::Seq::PrimedSeq Description

A representation of a sequence and two primers flanking a target region Bio::Seq::PrimedSeq is a representation of a sequence and two primers flanking a target region.SYNOPSIS # The easiest way to use this is probably either, (i), get the # output from Bio::Tools::Run::Primer3, Bio::Tools::Primer3, or # Bio::Tools::PCRSimulation: # For example, start with a fasta file use Bio::SeqIO; use Bio::Tools::Run::Primer3; my $file = shift || die "need a file to read"; my $seqin = Bio::SeqIO->new(-file => $file); my $seq = $seqin->next_seq; # use primer3 to design some primers my $primer3run = Bio::Tools::Run::Primer3->new(-seq => $seq); $primer3run -> run; # run it with the default parameters # create a file to write the results to my $seqout = Bio::SeqIO->new(-file => ">primed_sequence.gbk", -format => 'genbank'); # now just get all the results and write them out. while (my $results = $primer3run->next_primer) { $seqout->write_seq($results->annotated_seq); } # Or, (ii), to create a genbank file for a sequence and its cognate # primers: use Bio::SeqIO; use Bio::Seq::PrimedSeq; # have a sequence file ($file) with the template, and two primers # that match it, in fasta format my $file = shift || die "$0 "; my $seqin = Bio::SeqIO->new(-file => $file); # read three sequences my ($template, $leftprimer, $rightprimer) = ($seqin->next_seq, $seqin->next_seq, $seqin->next_seq); # set up the primed sequence object my $primedseq = Bio::Seq::PrimedSeq->new(-seq => $template, -left_primer => $leftprimer, -right_primer => $rightprimer); # open a file for output my $seqout = Bio::SeqIO->new(-file => ">primed_sequence.gbk", -format => 'genbank'); # print the sequence out $seqout->write_seq($primedseq->annotated_sequence); # This should output a genbank file with the two primers labeled.This module is a slightly glorified capsule containing a primed sequence. It was created to address the fact that a primer is more than a seqfeature and there need to be ways to represent the primer-sequence complex and the behaviors and attributes that are associated with the complex. Requirements: · Perl

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