Bio::Tools::Primer3Redux::Primer
# get the Bio::Tools::Primer3Redux::Primer through Bio::Tools::Primer3Redux... # dies with an error if no sequence is attached, or if sequence region # does not match cached sequence from Primer3. Useful if decorating an already # generated Bio::Seq with primers. $primer->validate_seq; my $seq = $primer->seq; # Bio::Seq object if ($primer->melting_temp < 55) { warn "Primer ".$primer->display_name." is below optimal temp"; } # if primer3 EXPLAIN settings are used... print "Run parameters:".$primer->run_description."\n";
This class is a simple subclass of Bio::SeqFeature::Generic that adds convenience accessor methods for primer-specific data, such as Tm, GC content, and other interesting bits of information returned from Primer3. Beyond that, the data can be persisted just as any Bio::SeqFeatureI; it doesn't add any additional primary attributes that may not be persisted effectively.
Bio::Tools::Primer3Redux::Primer - Simple Decorator of a Bio::SeqFeature::Generic with convenience methods for retrieving Tm, GC, validating primer seq against attached sequence, etc.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : oligo_type Usage : $obj->oligo_type Function : get/set the oligo type Returns : the oligo type (forward_primer, reverse_primer, internal_oligo) Args : optional string Note : simple alias for primary_tag
Title : rank Usage : $obj->rank Function : get/set the rank Returns : rank Args : optional string
Title : validate_seq Usage : $obj->validate_seq Function : Checks the calculated primer sequence against the actual sequence being analysed. Returns : True (1) if validated, False (0) and a warning otherwise Args : none
Title : melting_temp Usage : $obj->melting_temp Function : returns the Tm calculated for the primer via Primer3 Returns : float Args : optional Tm (possibly calculated via other means)
Title : gc Usage : $obj->gc Function : returns the GC content calculated for the primer via Primer3 Returns : float (percent) Args : optional GC content (possibly calculated via other means)
Title : run_description Usage : $obj->run_description Function : returns the run description for this primer (via Primer3) Returns : string Args : optional description
cjfields <cjfields@bioperl.org>
This software is copyright (c) 2011 by Chris Fields.
This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.
To install Bio::Tools::Primer3Redux, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Tools::Primer3Redux
CPAN shell
perl -MCPAN -e shell install Bio::Tools::Primer3Redux
For more information on module installation, please visit the detailed CPAN module installation guide.