File Coverage

Bio/SeqFeature/Primer.pm
Criterion Covered Total %
statement 64 66 96.9
branch 13 14 92.8
condition n/a
subroutine 8 8 100.0
pod 4 4 100.0
total 89 92 96.7


line stmt bran cond sub pod time code
1             #
2             # BioPerl module for Bio::SeqFeature::Primer
3             #
4             # This is the original copyright statement. I have relied on Chad's module
5             # extensively for this module.
6             #
7             # Copyright (c) 1997-2001 bioperl, Chad Matsalla. All Rights Reserved.
8             # This module is free software; you can redistribute it and/or
9             # modify it under the same terms as Perl itself.
10             #
11             # Copyright Chad Matsalla
12             #
13             # You may distribute this module under the same terms as perl itself
14             # POD documentation - main docs before the code
15             #
16             # But I have modified lots of it, so I guess I should add:
17             #
18             # Copyright (c) 2003 bioperl, Rob Edwards. All Rights Reserved.
19             # This module is free software; you can redistribute it and/or
20             # modify it under the same terms as Perl itself.
21             #
22             # Copyright Rob Edwards
23             #
24             # You may distribute this module under the same terms as perl itself
25             # POD documentation - main docs before the code
26              
27             =head1 NAME
28              
29             Bio::SeqFeature::Primer - Primer Generic SeqFeature
30              
31             =head1 SYNOPSIS
32              
33             use Bio::SeqFeature::Primer;
34              
35             # Primer object with explicitly-defined sequence object or sequence string
36             my $primer = Bio::SeqFeature::Primer->new( -seq => 'ACGTAGCT' );
37             $primer->display_name('test_id');
38             print "These are the details of the primer:\n".
39             "Name: ".$primer->display_name."\n".
40             "Tag: ".$primer->primary_tag."\n". # always 'Primer'
41             "Sequence: ".$primer->seq->seq."\n".
42             "Tm: ".$primer->Tm."\n\n"; # melting temperature
43              
44             # Primer object with implicit sequence object
45             # It is a lighter approach for when the primer location on a template is known
46             use Bio::Seq;
47             my $template = Bio::Seq->new( -seq => 'ACGTAGCTCTTTTCATTCTGACTGCAACG' );
48             $primer = Bio::SeqFeature::Primer->new( -start => 1, -end =>5, -strand => 1 );
49             $template->add_SeqFeature($primer);
50             print "Primer sequence is: ".$primer->seq->seq."\n";
51             # Primer sequence is 'ACGTA'
52              
53             =head1 DESCRIPTION
54              
55             This module handles PCR primer sequences. The L object
56             is a L object that can additionally contain a primer
57             sequence and its coordinates on a template sequence. The primary_tag() for this
58             object is 'Primer'. A method is provided to calculate the melting temperature Tm
59             of the primer. L objects are useful to build
60             L amplicon objects such as the ones returned by
61             L.
62              
63             =head1 FEEDBACK
64              
65             =head2 Mailing Lists
66              
67             User feedback is an integral part of the evolution of this and other
68             Bioperl modules. Send your comments and suggestions preferably to one
69             of the Bioperl mailing lists. Your participation is much appreciated.
70              
71             bioperl-l@bioperl.org - General discussion
72             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
73              
74             =head2 Support
75              
76             Please direct usage questions or support issues to the mailing list:
77              
78             I
79              
80             rather than to the module maintainer directly. Many experienced and
81             reponsive experts will be able look at the problem and quickly
82             address it. Please include a thorough description of the problem
83             with code and data examples if at all possible.
84              
85             =head2 Reporting Bugs
86              
87             Report bugs to the Bioperl bug tracking system to help us keep track
88             the bugs and their resolution. Bug reports can be submitted via the
89             web:
90              
91             https://github.com/bioperl/bioperl-live/issues
92              
93             =head1 AUTHOR
94              
95             Rob Edwards, redwards@utmem.edu
96              
97             The original concept and much of the code was written by
98             Chad Matsalla, bioinformatics1@dieselwurks.com
99              
100             =head1 APPENDIX
101              
102             The rest of the documentation details each of the object
103             methods. Internal methods are usually preceded with a _
104              
105             =cut
106              
107              
108             package Bio::SeqFeature::Primer;
109              
110 5     5   2107 use strict;
  5         6  
  5         111  
111 5     5   606 use Bio::PrimarySeq;
  5         56  
  5         177  
112 5     5   1622 use Bio::Tools::SeqStats;
  5         7  
  5         117  
113              
114 5     5   22 use base qw(Bio::SeqFeature::SubSeq);
  5         7  
  5         1427  
115              
116              
117             =head2 new()
118              
119             Title : new()
120             Usage : my $primer = Bio::SeqFeature::Primer( -seq => $seq_object );
121             Function: Instantiate a new Bio::SeqFeature::Primer object
122             Returns : A Bio::SeqFeature::Primer object
123             Args : -seq , a sequence object or a sequence string (optional)
124             -id , the ID to give to the primer sequence, not feature (optional)
125              
126             =cut
127              
128             sub new {
129 40     40 1 109 my ($class, %args) = @_;
130              
131             # Legacy stuff
132 40         63 my $sequence = delete $args{-sequence};
133 40 100       57 if ($sequence) {
134 1         10 Bio::Root::Root->deprecated(
135             -message => 'Creating a Bio::SeqFeature::Primer with -sequence is deprecated. Use -seq instead.',
136             -warn_version => '1.006',
137             -throw_version => '1.008',
138             );
139 1         5 $args{-seq} = $sequence;
140             }
141              
142             # Initialize Primer object
143 40         117 my $self = $class->SUPER::new(%args);
144 40         120 my ($id) = $self->_rearrange([qw(ID)], %args);
145 40 100       105 $id && $self->seq->id($id);
146 40         90 $self->primary_tag('Primer');
147 40         90 return $self;
148             }
149              
150              
151             # Bypass B::SF::Generic's location() when a string is passed (for compatibility)
152              
153             sub location {
154 181     181 1 127 my ($self, $location) = @_;
155 181 100       234 if ($location) {
156 1 50       3 if ( not ref $location ) {
157             # Use location as a string for backward compatibility
158 1         6 Bio::Root::Root->deprecated(
159             -message => 'Passing a string to location() is deprecated. Pass a Bio::Location::Simple object or use start() and end() instead.',
160             -warn_version => '1.006',
161             -throw_version => '1.008',
162             );
163 1         5 $self->{'_location'} = $location;
164             } else {
165 0         0 $self->SUPER::location($location);
166             }
167             }
168 181         248 return $self->SUPER::location;
169             }
170              
171              
172             =head2 Tm()
173              
174             Title : Tm()
175             Usage : my $tm = $primer->Tm(-salt => 0.05, -oligo => 0.0000001);
176             Function: Calculate the Tm (melting temperature) of the primer
177             Returns : A scalar containing the Tm.
178             Args : -salt : set the Na+ concentration on which to base the calculation
179             (default=0.05 molar).
180             : -oligo : set the oligo concentration on which to base the
181             calculation (default=0.00000025 molar).
182             Notes : Calculation of Tm as per Allawi et. al Biochemistry 1997
183             36:10581-10594. Also see documentation at
184             http://www.idtdna.com/Scitools/Scitools.aspx as they use this
185             formula and have a couple nice help pages. These Tm values will be
186             about are about 0.5-3 degrees off from those of the idtdna web tool.
187             I don't know why.
188              
189             This was suggested by Barry Moore (thanks!). See the discussion on
190             the bioperl-l with the subject "Bio::SeqFeature::Primer Calculating
191             the PrimerTM"
192              
193             =cut
194              
195             sub Tm {
196 2     2 1 4 my ($self, %args) = @_;
197 2         2 my $salt_conc = 0.05; # salt concentration (molar units)
198 2         3 my $oligo_conc = 0.00000025; # oligo concentration (molar units)
199 2 100       5 if ($args{'-salt'}) {
200             # Accept object defined salt concentration
201 1         2 $salt_conc = $args{'-salt'};
202             }
203 2 100       4 if ($args{'-oligo'}) {
204             # Accept object defined oligo concentration
205 1         2 $oligo_conc = $args{'-oligo'};
206             }
207 2         4 my $seqobj = $self->seq();
208 2         4 my $length = $seqobj->length();
209 2         4 my $sequence = uc $seqobj->seq();
210 2         3 my @dinucleotides;
211             my $enthalpy;
212 0         0 my $entropy;
213             # Break sequence string into an array of all possible dinucleotides
214 2         10 while ($sequence =~ /(.)(?=(.))/g) {
215 40         81 push @dinucleotides, $1.$2;
216             }
217             # Build a hash with the thermodynamic values
218 2         36 my %thermo_values = ('AA' => {'enthalpy' => -7.9,
219             'entropy' => -22.2},
220             'AC' => {'enthalpy' => -8.4,
221             'entropy' => -22.4},
222             'AG' => {'enthalpy' => -7.8,
223             'entropy' => -21},
224             'AT' => {'enthalpy' => -7.2,
225             'entropy' => -20.4},
226             'CA' => {'enthalpy' => -8.5,
227             'entropy' => -22.7},
228             'CC' => {'enthalpy' => -8,
229             'entropy' => -19.9},
230             'CG' => {'enthalpy' => -10.6,
231             'entropy' => -27.2},
232             'CT' => {'enthalpy' => -7.8,
233             'entropy' => -21},
234             'GA' => {'enthalpy' => -8.2,
235             'entropy' => -22.2},
236             'GC' => {'enthalpy' => -9.8,
237             'entropy' => -24.4},
238             'GG' => {'enthalpy' => -8,
239             'entropy' => -19.9},
240             'GT' => {'enthalpy' => -8.4,
241             'entropy' => -22.4},
242             'TA' => {'enthalpy' => -7.2,
243             'entropy' => -21.3},
244             'TC' => {'enthalpy' => -8.2,
245             'entropy' => -22.2},
246             'TG' => {'enthalpy' => -8.5,
247             'entropy' => -22.7},
248             'TT' => {'enthalpy' => -7.9,
249             'entropy' => -22.2},
250             'A' => {'enthalpy' => 2.3,
251             'entropy' => 4.1},
252             'C' => {'enthalpy' => 0.1,
253             'entropy' => -2.8},
254             'G' => {'enthalpy' => 0.1,
255             'entropy' => -2.8},
256             'T' => {'enthalpy' => 2.3,
257             'entropy' => 4.1}
258             );
259             # Loop through dinucleotides and calculate cumulative enthalpy and entropy values
260 2         5 for (@dinucleotides) {
261 40         31 $enthalpy += $thermo_values{$_}{enthalpy};
262 40         28 $entropy += $thermo_values{$_}{entropy};
263             }
264             # Account for initiation parameters
265 2         5 $enthalpy += $thermo_values{substr($sequence, 0, 1)}{enthalpy};
266 2         3 $entropy += $thermo_values{substr($sequence, 0, 1)}{entropy};
267 2         3 $enthalpy += $thermo_values{substr($sequence, -1, 1)}{enthalpy};
268 2         2 $entropy += $thermo_values{substr($sequence, -1, 1)}{entropy};
269             # Symmetry correction
270 2         2 $entropy -= 1.4;
271 2         2 my $r = 1.987; # molar gas constant
272 2         8 my $tm = $enthalpy * 1000 / ($entropy + ($r * log($oligo_conc))) - 273.15 + (12* (log($salt_conc)/log(10)));
273              
274 2         18 return $tm;
275             }
276              
277             =head2 Tm_estimate
278              
279             Title : Tm_estimate
280             Usage : my $tm = $primer->Tm_estimate(-salt => 0.05);
281             Function: Estimate the Tm (melting temperature) of the primer
282             Returns : A scalar containing the Tm.
283             Args : -salt set the Na+ concentration on which to base the calculation.
284             Notes : This is only an estimate of the Tm that is kept in for comparative
285             reasons. You should probably use Tm instead!
286              
287             This Tm calculations are taken from the Primer3 docs: They are
288             based on Bolton and McCarthy, PNAS 84:1390 (1962)
289             as presented in Sambrook, Fritsch and Maniatis,
290             Molecular Cloning, p 11.46 (1989, CSHL Press).
291              
292             Tm = 81.5 + 16.6(log10([Na+])) + .41*(%GC) - 600/length
293              
294             where [Na+] is the molar sodium concentration, %GC is the
295             %G+C of the sequence, and length is the length of the sequence.
296              
297             However.... I can never get this calculation to give me the same result
298             as primer3 does. Don't ask why, I never figured it out. But I did
299             want to include a Tm calculation here because I use these modules for
300             other things besides reading primer3 output.
301              
302             The primer3 calculation is saved as 'PRIMER_LEFT_TM' or 'PRIMER_RIGHT_TM'
303             and this calculation is saved as $primer->Tm so you can get both and
304             average them!
305              
306             =cut
307              
308             sub Tm_estimate {
309              
310             # This should probably be put into seqstats as it is more generic, but what the heck.
311              
312 2     2 1 4 my ($self, %args) = @_;
313 2         3 my $salt = 0.2;
314 2 100       5 if ($args{'-salt'}) {
315 1         2 $salt = $args{'-salt'}
316             };
317 2         5 my $seqobj = $self->seq();
318 2         5 my $length = $seqobj->length();
319 2         11 my $seqdata = Bio::Tools::SeqStats->count_monomers($seqobj);
320 2         2 my $gc=$$seqdata{'G'} + $$seqdata{'C'};
321 2         5 my $percent_gc = ($gc/$length)*100;
322              
323 2         5 my $tm = 81.5+(16.6*(log($salt)/log(10)))+(0.41*$percent_gc) - (600/$length);
324              
325 2         9 return $tm;
326             }
327              
328             =head2 primary_tag, source_tag, location, start, end, strand...
329              
330             The documentation of L describes all the methods that
331             L object inherit.
332              
333             =cut
334              
335             1;