Bio::SeqFeature::Amplicon - Amplicon feature
# Amplicon with explicit sequence use Bio::SeqFeature::Amplicon; my $amplicon = Bio::SeqFeature::Amplicon->new( -seq => $seq_object, -fwd_primer => $primer_object_1, -rev_primer => $primer_object_2, ); # Amplicon with implicit sequence use Bio::Seq; my $template = Bio::Seq->new( -seq => 'AAAAACCCCCGGGGGTTTTT' ); $amplicon = Bio::SeqFeature::Amplicon->new( -start => 6, -end => 15, ); $template->add_SeqFeature($amplicon); print "Amplicon start : ".$amplicon->start."\n"; print "Amplicon end : ".$amplicon->end."\n"; print "Amplicon sequence: ".$amplicon->seq->seq."\n"; # Amplicon sequence should be 'CCCCCGGGGG'
Bio::SeqFeature::Amplicon extends Bio::SeqFeature::Subseq to represent an amplicon sequence and optional primer sequences.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new() Usage : my $amplicon = Bio::SeqFeature::Amplicon( -seq => $seq_object ); Function: Instantiate a new Bio::SeqFeature::Amplicon object Args : -seq , the sequence object or sequence string of the amplicon (optional) -fwd_primer , a Bio::SeqFeature primer object with specified location on amplicon (optional) -rev_primer , a Bio::SeqFeature primer object with specified location on amplicon (optional) Returns : A Bio::SeqFeature::Amplicon object
Title : fwd_primer Usage : my $primer = $feat->fwd_primer(); Function: Get or set the forward primer. When setting it, the primary tag 'fwd_primer' is added to the primer and its start, stop and strand attributes are set if needed, assuming that the forward primer is at the beginning of the amplicon and the reverse primer at the end. Args : A Bio::SeqFeature::Primer object (optional) Returns : A Bio::SeqFeature::Primer object
Title : rev_primer Usage : my $primer = $feat->rev_primer(); Function: Get or set the reverse primer. When setting it, the primary tag 'rev_primer' is added to the primer. Args : A Bio::SeqFeature::Primer object (optional) Returns : A Bio::SeqFeature::Primer object