NAME

Bio::Tools::Primer3Redux::Primer

SYNOPSIS

# 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";

DESCRIPTION

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.

NAME

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.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

http://bugzilla.open-bio.org/

AUTHOR - Chris Fields

Email cjfields at bioperl dot org

Describe contact details here

CONTRIBUTORS

Additional contributors names and emails here

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

oligo_type

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

rank

Title    : rank
Usage    : $obj->rank
Function : get/set the rank
Returns  : rank
Args     : optional string

validate_seq

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

melting_temp

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)

gc_content

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)

run_description

Title    : run_description
Usage    : $obj->run_description
Function : returns the run description for this primer (via Primer3)
Returns  : string
Args     : optional description

AUTHOR

cjfields <cjfields@bioperl.org>

COPYRIGHT AND LICENSE

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.

cpanm Bio::Tools::Primer3Redux

perl -MCPAN -e shell
install Bio::Tools::Primer3Redux