Christopher Fields > Bio-Tools-Primer3Redux-0.09 > Bio::Tools::Primer3Redux::Primer

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Module Version: 0.09   Source  

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.

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