qu-thermo 1.0.0
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +7 -0
- data/.gitignore +17 -0
- data/Gemfile +4 -0
- data/LICENSE.txt +22 -0
- data/README.md +29 -0
- data/Rakefile +1 -0
- data/lib/qu/thermo.rb +69 -0
- data/lib/qu/thermo/parameters.rb +283 -0
- data/lib/qu/thermo/version.rb +5 -0
- data/qu-thermo.gemspec +23 -0
- metadata +81 -0
checksums.yaml
ADDED
@@ -0,0 +1,7 @@
|
|
1
|
+
---
|
2
|
+
SHA1:
|
3
|
+
metadata.gz: c76137b4b3ca987df2112ff6ed774e2aace0be69
|
4
|
+
data.tar.gz: bb0c6b08e3b262344a3a441f069a812797c0450b
|
5
|
+
SHA512:
|
6
|
+
metadata.gz: 3af235456aad35965f49abeda1771313a27122ec846bc029d55ebf434ce82286588783796c5f7f022e38596ba41fe0ec29f7fa91f70a9542df966a18ffd9eeea
|
7
|
+
data.tar.gz: 97420eaaeb38f51cbfdab5be8974e90769b031eb4c3a2fa6d623c4f8e6bafc7a5687d6415b94fa02a6fdc5a6016d7063fd7a88a9d5a84246b682a7dc3ad41671
|
data/.gitignore
ADDED
data/Gemfile
ADDED
data/LICENSE.txt
ADDED
@@ -0,0 +1,22 @@
|
|
1
|
+
Copyright (c) 2013 Wubin Qu
|
2
|
+
|
3
|
+
MIT License
|
4
|
+
|
5
|
+
Permission is hereby granted, free of charge, to any person obtaining
|
6
|
+
a copy of this software and associated documentation files (the
|
7
|
+
"Software"), to deal in the Software without restriction, including
|
8
|
+
without limitation the rights to use, copy, modify, merge, publish,
|
9
|
+
distribute, sublicense, and/or sell copies of the Software, and to
|
10
|
+
permit persons to whom the Software is furnished to do so, subject to
|
11
|
+
the following conditions:
|
12
|
+
|
13
|
+
The above copyright notice and this permission notice shall be
|
14
|
+
included in all copies or substantial portions of the Software.
|
15
|
+
|
16
|
+
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
17
|
+
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
|
18
|
+
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
19
|
+
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
|
20
|
+
LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
|
21
|
+
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
|
22
|
+
WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
data/README.md
ADDED
@@ -0,0 +1,29 @@
|
|
1
|
+
# Qu::Thermo
|
2
|
+
|
3
|
+
A thermodynamics library for calculating DNA/DNA binding energy
|
4
|
+
|
5
|
+
## Installation
|
6
|
+
|
7
|
+
Add this line to your application's Gemfile:
|
8
|
+
|
9
|
+
gem 'qu-thermo'
|
10
|
+
|
11
|
+
And then execute:
|
12
|
+
|
13
|
+
$ bundle
|
14
|
+
|
15
|
+
Or install it yourself as:
|
16
|
+
|
17
|
+
$ gem install qu-thermo
|
18
|
+
|
19
|
+
## Usage
|
20
|
+
|
21
|
+
`tm = Qu::Thermo::Hybrid.new(seq_1, seq_2).tm`
|
22
|
+
|
23
|
+
## Contributing
|
24
|
+
|
25
|
+
1. Fork it
|
26
|
+
2. Create your feature branch (`git checkout -b my-new-feature`)
|
27
|
+
3. Commit your changes (`git commit -am 'Add some feature'`)
|
28
|
+
4. Push to the branch (`git push origin my-new-feature`)
|
29
|
+
5. Create new Pull Request
|
data/Rakefile
ADDED
@@ -0,0 +1 @@
|
|
1
|
+
require "bundler/gem_tasks"
|
data/lib/qu/thermo.rb
ADDED
@@ -0,0 +1,69 @@
|
|
1
|
+
require "qu/thermo/version"
|
2
|
+
require_relative "thermo/parameters"
|
3
|
+
|
4
|
+
|
5
|
+
module Qu
|
6
|
+
module Thermo
|
7
|
+
class Hybrid
|
8
|
+
def initialize(qseq, sseq, mono=50, diva=1.5, dntp=0.25, oligo=50)
|
9
|
+
# qseq: 5' -> 3'
|
10
|
+
# sseq: 3' -> 5'
|
11
|
+
@qseq = qseq.upcase
|
12
|
+
@sseq = sseq.upcase
|
13
|
+
@mono = mono.to_f
|
14
|
+
@diva = diva.to_f
|
15
|
+
@dntp = dntp.to_f
|
16
|
+
@oligo = oligo.to_f
|
17
|
+
|
18
|
+
@dh, @ds = delta_hs
|
19
|
+
@adjusted_mono = (@mono + diva2mono) / 1000.0
|
20
|
+
@adjusted_ds = @ds + 0.368 * (@sseq.size - 1) * Math.log(@adjusted_mono, Math::E)
|
21
|
+
end
|
22
|
+
|
23
|
+
def dg
|
24
|
+
(@dh * 1000 - (273.15 + 37) * @adjusted_ds) / 1000.0
|
25
|
+
end
|
26
|
+
|
27
|
+
def tm
|
28
|
+
@dh * 1000.0 / (@adjusted_ds + 1.987 * Math.log(@oligo / 1000000000.0 / 4, Math::E)) - 273.15
|
29
|
+
end
|
30
|
+
|
31
|
+
def dg_tm
|
32
|
+
return dg, tm
|
33
|
+
end
|
34
|
+
|
35
|
+
private
|
36
|
+
|
37
|
+
def diva2mono
|
38
|
+
@dntp = 0 if @diva == 0
|
39
|
+
|
40
|
+
$stderr.puts "Error conc for diva and mono" if @diva < 0 or @dntp < 0
|
41
|
+
|
42
|
+
@diva = @dntp if @diva < @dntp
|
43
|
+
|
44
|
+
return 120 * (Math.sqrt(@diva - @dntp))
|
45
|
+
end
|
46
|
+
|
47
|
+
def delta_hs
|
48
|
+
init_start = "init#{@qseq[0]}#{@sseq[0]}"
|
49
|
+
init_stop = "init#{@qseq[-1]}#{@sseq[-1]}"
|
50
|
+
|
51
|
+
dh = ds = 0
|
52
|
+
if DH.include?(init_start) and DH.include?(init_stop)
|
53
|
+
dh = DH[init_start] + DH[init_stop]
|
54
|
+
ds = DS[init_start] + DS[init_stop]
|
55
|
+
end
|
56
|
+
|
57
|
+
(0...(@qseq.size - 1)).each do |i|
|
58
|
+
dinuc = "#{@qseq[i...(i+2)]}#{@sseq[i...(i+2)]}"
|
59
|
+
if DH.include?(dinuc) and DS.include?(dinuc)
|
60
|
+
dh += DH[dinuc]
|
61
|
+
ds += DS[dinuc]
|
62
|
+
end
|
63
|
+
end
|
64
|
+
|
65
|
+
return dh, ds
|
66
|
+
end
|
67
|
+
end
|
68
|
+
end
|
69
|
+
end
|
@@ -0,0 +1,283 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
# -*- coding: utf-8 -*- #
|
3
|
+
=begin
|
4
|
+
Thermodynamics Parameters for calculating Tm and Gibbs free energy
|
5
|
+
|
6
|
+
References
|
7
|
+
|
8
|
+
Matched base-pair =>
|
9
|
+
|
10
|
+
[1] SantaLucia JR (1998) "A unified view of polymer, dumbbell
|
11
|
+
and oligonucleotide DNA nearest-neighbor thermodynamics", Proc Natl
|
12
|
+
Acad Sci 95=>1460-65 http=>//dx.doi.org/10.1073/pnas.95.4.1460.
|
13
|
+
|
14
|
+
Mismatched base-pair =>
|
15
|
+
|
16
|
+
[1]. Allawi, H.T. and SantaLucia, J. (1997) Thermodynamics and NMR
|
17
|
+
of internal GT mismatches in DNA, Biochemistry, 36, 10581-10594.
|
18
|
+
[2]. Allawi, H.T. and SantaLucia, J. (1998) Nearest-neighbor
|
19
|
+
thermodynamics of internal A center dot C mismatches in
|
20
|
+
DNA=> Sequence dependence and pH effects, Biochemistry, 37, 9435-9444.
|
21
|
+
[3]. Allawi, H.T. and SantaLucia, J. (1998) Nearest neighbor
|
22
|
+
thermodynamic parameters for internal G center dot A mismatches
|
23
|
+
in DNA, Biochemistry, 37, 2170-2179.
|
24
|
+
[4]. Allawi, H.T. and Santalucia, J. (1998) Thermodynamics of
|
25
|
+
internal C center dot T mismatches in DNA, Nucleic Acids
|
26
|
+
Research, 26, 2694-2701.
|
27
|
+
|
28
|
+
NN model =>
|
29
|
+
|
30
|
+
[1] SantaLucia, J. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics, Proceedings of the National Academy of Sci-ences of the United States of America, 95, 1460-1465.
|
31
|
+
|
32
|
+
[2] von Ahsen, N., Wittwer, C.T. and Schutz, E. (2001) Oligonucleotide melting tempera-tures under PCR conditions=> Nearest-neighbor corrections for Mg2+, deoxynu-cleotide triphosphate, and dimethyl sulfoxide concentrations with comparison to alternative empirical formulas, Clinical Chemistry, 47, 1956-1961.
|
33
|
+
|
34
|
+
by Wubin Qu <quwubin@gmail.com>
|
35
|
+
Copyright @ 2010, All Rights Reserved.
|
36
|
+
=end
|
37
|
+
|
38
|
+
module Qu
|
39
|
+
module Thermo
|
40
|
+
DH = {
|
41
|
+
'AATT' => -7.9, 'TTAA' => -7.9,
|
42
|
+
'ATTA' => -7.2, 'TAAT' => -7.2,
|
43
|
+
'CAGT' => -8.5, 'TGAC' => -8.5,
|
44
|
+
'GTCA' => -8.4, 'ACTG' => -8.4,
|
45
|
+
'CTGA' => -7.8, 'AGTC' => -7.8,
|
46
|
+
'GACT' => -8.2, 'TCAG' => -8.2,
|
47
|
+
'CGGC' => -10.6, 'GCCG' => -9.8,
|
48
|
+
'GGCC' => -8.0, 'CCGG' => -8.0,
|
49
|
+
'initCG' => 0.1, 'initGC' => 0.1,
|
50
|
+
'initAT' => 2.3, 'initTA' => 2.3,
|
51
|
+
# Like pair mismatches
|
52
|
+
'AATA' => 1.2, 'ATAA' => 1.2,
|
53
|
+
'CAGA' => -0.9, 'AGAC' => -0.9,
|
54
|
+
'GACA' => -2.9, 'ACAG' => -2.9,
|
55
|
+
'TAAA' => 4.7, 'AAAT' => 4.7,
|
56
|
+
'ACTC' => 0.0, 'CTCA' => 0.0,
|
57
|
+
'CCGC' => -1.5, 'CGCC' => -1.5,
|
58
|
+
'GCCC' => 3.6, 'CCCG' => 3.6,
|
59
|
+
'TCAC' => 6.1, 'CACT' => 6.1,
|
60
|
+
'AGTG' => -3.1, 'GTGA' => -3.1,
|
61
|
+
'CGGG' => -4.9, 'GGGC' => -4.9,
|
62
|
+
'GGCG' => -6.0, 'GCGG' => -6.0,
|
63
|
+
'TGAG' => 1.6, 'GAGT' => 1.6,
|
64
|
+
'ATTT' => -2.7, 'TTTA' => -2.7,
|
65
|
+
'CTGT' => -5.0, 'TGTC' => -5.0,
|
66
|
+
'GTCT' => -2.2, 'TCTG' => -2.2,
|
67
|
+
'TTAT' => 0.2, 'TATT' => 0.2,
|
68
|
+
# G.T mismatches
|
69
|
+
'AGTT' => 1.0, 'TTGA' => 1.0,
|
70
|
+
'ATTG' => -2.5, 'GTTA' => -2.5,
|
71
|
+
'CGGT' => -4.1, 'TGGC' => -4.1,
|
72
|
+
'CTGG' => -2.8, 'GGTC' => -2.8,
|
73
|
+
'GGCT' => 3.3, 'TCGG' => 3.3,
|
74
|
+
'GGTT' => 5.8, 'TTGG' => 5.8,
|
75
|
+
'GTCG' => -4.4, 'GCTG' => -4.4,
|
76
|
+
'GTTG' => 4.1, 'GTTG' => 4.1,
|
77
|
+
'TGAT' => -0.1, 'TAGT' => -0.1,
|
78
|
+
'TGGT' => -1.4, 'TGGT' => -1.4,
|
79
|
+
'TTAG' => -1.3, 'GATT' => -1.3,
|
80
|
+
#G.A mismatches
|
81
|
+
'AATG' => -0.6, 'GTAA' => -0.6,
|
82
|
+
'AGTA' => -0.7, 'ATGA' => -0.7,
|
83
|
+
'CAGG' => -0.7, 'GGAC' => -0.7,
|
84
|
+
'CGGA' => -4.0, 'AGGC' => -4.0,
|
85
|
+
'GACG' => -0.6, 'GCAG' => -0.6,
|
86
|
+
'GGCA' => 0.5, 'ACGG' => 0.5,
|
87
|
+
'TAAG' => 0.7, 'GAAT' => 0.7,
|
88
|
+
'TGAA' => 3.0, 'AAGT' => 3.0,
|
89
|
+
#C.T mismatches
|
90
|
+
'ACTT' => 0.7, 'TTCA' => 0.7,
|
91
|
+
'ATTC' => -1.2, 'CTTA' => -1.2,
|
92
|
+
'CCGT' => -0.8, 'TGCC' => -0.8,
|
93
|
+
'CTGC' => -1.5, 'CGTC' => -1.5,
|
94
|
+
'GCCT' => 2.3, 'TCCG' => 2.3,
|
95
|
+
'GTCC' => 5.2, 'CCTG' => 5.2,
|
96
|
+
'TCAT' => 1.2, 'TACT' => 1.2,
|
97
|
+
'TTAC' => 1.0, 'CATT' => 1.0,
|
98
|
+
#A.C mismatches
|
99
|
+
'AATC' => 2.3, 'CTAA'=>2.3,
|
100
|
+
'ACTA' => 5.3, 'ATCA'=>5.3,
|
101
|
+
'CAGC' => 1.9, 'CGAC'=>1.9,
|
102
|
+
'CCGA' => 0.6, 'AGCC'=>0.6,
|
103
|
+
'GACC' => 5.2, 'CCAG'=>5.2,
|
104
|
+
'GCCA' => -0.7, 'ACCG'=>-0.7,
|
105
|
+
'TAAC' => 3.4, 'CAAT'=>3.4,
|
106
|
+
'TCAA' => 7.6, 'AACT'=>7.6,
|
107
|
+
|
108
|
+
#tandem mismatch
|
109
|
+
'GGTT' => 5.8, 'TTGG' => 5.8,
|
110
|
+
'GTTG' => 4.1, 'TGGT' => -1.4,
|
111
|
+
'GTTT' => 5.8, 'TTTG' => 5.8,
|
112
|
+
'GTAT' => -0.1, 'TATG' => -0.1,
|
113
|
+
#single bulge loop
|
114
|
+
'AAAT-T' => -4.0, 'AATT-A' => -13.5, 'AACT-G' => 10.2, 'AAGT-C' => -0.2,
|
115
|
+
'ATAT-T' => 9.8, 'ATTT-A' => -19.5, 'ATCT-G' => -4.8, 'ATGT-C' => 5.6,
|
116
|
+
'ACAT-T' => 6.1, 'ACTT-A' => -3.4, 'ACCT-G' => -29.1, 'ACGT-C' => -1.2,
|
117
|
+
'AGAT-T' => 15.5, 'AGTT-A' => 5.3, 'AGCT-G' => -7.2, 'AGGT-C' => 5.7,
|
118
|
+
'TAAA-T' => 15.3, 'TATA-A' => 19.8, 'TACA-G' => -2.3, 'TAGA-C' => 15,
|
119
|
+
'TTAA-T' => -2.7, 'TTTA-A' => -8.2, 'TTCA-G' => 8.8, 'TTGA-C' => 7.0,
|
120
|
+
'TCAA-T' => 1.6, 'TCTA-A' => 9.9, 'TCCA-G' => -15.2, 'TCGA-C' => -0.7,
|
121
|
+
'TGAA-T' => -12.3, 'TGTA-A' => 20.9, 'TGCA-G' => 2.6, 'TGGA-C' => -9.2,
|
122
|
+
'CAAG-T' => -14.4, 'CATG-A' => -7.0, 'CACG-G' => 4.3, 'CAGG-C' => -2.9,
|
123
|
+
'CTAG-T' => -18.7, 'CTTG-A' => -4.6, 'CTCG-G' => -14.5, 'CTGG-C' => -4.7,
|
124
|
+
'CCAG-T' => 5.8, 'CCTG-A' => -5.3, 'CCCG-G' => -2.6, 'CCGG-C' => 9.1,
|
125
|
+
'CGAG-T' => -14.7, 'CGTG-A' => 2.1, 'CGCG-G' => -4.4, 'CGGG-C' => -16.4,
|
126
|
+
'GAAC-T' => -6.8, 'GATC-A' => -9.8, 'GACC-G' => -4.8, 'GAGC-C' => -6.5,
|
127
|
+
'GTAC-T' => -7.4, 'GTTC-A' => 1.8, 'GTCC-G' => -12.3, 'GTGC-C' => -2.3,
|
128
|
+
'GCAC-T' => -2.1, 'GCTC-A' => -3.5, 'GCCC-G' => 0.4, 'GCGC-C' => 13.8,
|
129
|
+
'GGAC-T' => 2.7, 'GGTC-A' => -1.2, 'GGCC-G' => -1.7, 'GGGC-C' => 3.5,
|
130
|
+
# single dangling_end
|
131
|
+
'AA-T' => 0.2, 'TA-T' => -6.9, 'GA-T' => -1.1, 'CA-T' => 0.6,
|
132
|
+
'AC-G' => -6.3, 'TC-G' => -4.0, 'GC-G' => -5.1, 'CC-G' => -4.4,
|
133
|
+
'AG-C' => -3.7, 'TG-C' => -4.9, 'GG-C' => -3.9, 'CG-C' => -4.0,
|
134
|
+
'AT-A' => -2.9, 'TT-A' => -0.2, 'GT-A' => -4.2, 'CT-A' => -4.1,
|
135
|
+
'AAT-' => -0.5, 'ACT-' => 4.7, 'AGT-' => -4.1, 'ATT-' => -3.8,
|
136
|
+
'TAA-' => -0.7, 'TCA-' => 4.4, 'TGA-' => -1.6, 'TTA-' => 2.9,
|
137
|
+
'GAC-' => -2.1, 'GCC-' => -0.2, 'GGC-' => -3.9, 'GTC-' => -4.4,
|
138
|
+
'CAG-' => -5.9, 'CCG-' => -2.6, 'CGG-' => -3.2, 'CTG-' => -5.2,
|
139
|
+
# long dangling_end
|
140
|
+
'CAAG--' => -2.15, 'CAAAG---' => -3.3, 'CAAAAG----' => -4.85,
|
141
|
+
'TAAA--' => -1.0, 'TAAAA---' => -1.95, 'TAAAAA----' => -2.35,
|
142
|
+
'AAA--T' => -1.5, 'AAAA---T' => -1.75, 'AAAAA----T' => -3.95,
|
143
|
+
'AAG--C' => -0.25, 'AAAG---C' => -0.15, 'AAAAG----C' => -0.75,
|
144
|
+
}
|
145
|
+
|
146
|
+
#--------------------#
|
147
|
+
# deltaS (cal/K.mol) #
|
148
|
+
#--------------------#
|
149
|
+
DS = {
|
150
|
+
'AATT' => -22.2, 'TTAA'=>-22.2,
|
151
|
+
'ATTA' => -20.4, 'TAAT'=>-21.3,
|
152
|
+
'CAGT' => -22.7, 'TGAC'=>-22.7,
|
153
|
+
'GTCA' => -22.4, 'ACTG'=>-22.4,
|
154
|
+
'CTGA' => -21.0, 'AGTC'=>-21.0,
|
155
|
+
'GACT' => -22.2, 'TCAG'=>-22.2,
|
156
|
+
'CGGC' => -27.2, 'GCCG'=>-24.4,
|
157
|
+
'GGCC' => -19.9, 'CCGG'=>-19.9,
|
158
|
+
'initCG' => -2.8, 'initGC'=>-2.8,
|
159
|
+
'initAT' => 4.1, 'initTA'=>4.1,
|
160
|
+
'sym' => -1.4,
|
161
|
+
# => Like=>pair=>mismatches
|
162
|
+
'AATA' => 1.7, 'ATAA'=>1.7,
|
163
|
+
'CAGA' => -4.2, 'AGAC'=>-4.2,
|
164
|
+
'GACA' => -9.8, 'ACAG'=>-9.8,
|
165
|
+
'TAAA' => 12.9, 'AAAT'=>12.9,
|
166
|
+
'ACTC' => -4.4, 'CTCA'=>-4.4,
|
167
|
+
'CCGC' => -7.2, 'CGCC'=>-7.2,
|
168
|
+
'GCCC' => 8.9, 'CCCG'=>8.9,
|
169
|
+
'TCAC' => 16.4, 'CACT'=>16.4,
|
170
|
+
'AGTG' => -9.5, 'GTGA'=>-9.5,
|
171
|
+
'CGGG' => -15.3, 'GGGC'=>-15.3,
|
172
|
+
'GGCG' => -15.8, 'GCGG'=>-15.8,
|
173
|
+
'TGAG' => 3.6, 'GAGT'=>3.6,
|
174
|
+
'ATTT' => -10.8, 'TTTA'=>-10.8,
|
175
|
+
'CTGT' => -15.8, 'TGTC'=>-15.8,
|
176
|
+
'GTCT' => -8.4, 'TCTG'=>-8.4,
|
177
|
+
'TTAT' => -1.5, 'TATT'=>-1.5,
|
178
|
+
# => G.T=>mismatches
|
179
|
+
'AGTT' => 0.9, 'TTGA'=>0.9,
|
180
|
+
'ATTG' => -8.3, 'GTTA'=>-8.3,
|
181
|
+
'CGGT' => -11.7, 'TGGC'=>-11.7,
|
182
|
+
'CTGG' => -8.0, 'GGTC'=>-8.0,
|
183
|
+
'GGCT' => 10.4, 'TCGG'=>10.4,
|
184
|
+
'GGTT' => 16.3, 'TTGG'=>16.3,
|
185
|
+
'GTCG' => -12.3, 'GCTG'=>-12.3,
|
186
|
+
'GTTG' => 9.5, 'GTTG'=>9.5,
|
187
|
+
'TGAT' => -1.7, 'TAGT'=>-1.7,
|
188
|
+
'TGGT' => -6.2, 'TGGT'=>-6.2,
|
189
|
+
'TTAG' => -5.3, 'GATT'=>-5.3,
|
190
|
+
# G.A mismatches
|
191
|
+
'AATG' => -2.3, 'GTAA' => -2.3,
|
192
|
+
'AGTA' => -2.3, 'ATGA' => -2.3,
|
193
|
+
'CAGG' => -2.3, 'GGAC' => -2.3,
|
194
|
+
'CGGA' => -13.2, 'AGGC' => -13.2,
|
195
|
+
'GACG' => -1.0, 'GCAG' => -1.0,
|
196
|
+
'GGCA' => 3.2, 'ACGG' => 3.2,
|
197
|
+
'TAAG' => 0.7, 'GAAT' => 0.7,
|
198
|
+
'TGAA' => 7.4, 'AAGT' => 7.4,
|
199
|
+
# C.T mismatches
|
200
|
+
'ACTT' => 0.2, 'TTCA' => 0.2,
|
201
|
+
'ATTC' => -6.2, 'CTTA' => -6.2,
|
202
|
+
'CCGT' => -4.5, 'TGCC' => -4.5,
|
203
|
+
'CTGC' => -6.1, 'CGTC' => -6.1,
|
204
|
+
'GCCT' => 5.4, 'TCCG' => 5.4,
|
205
|
+
'GTCC' => 13.5, 'CCTG' => 13.5,
|
206
|
+
'TCAT' => 0.7, 'TACT' => 0.7,
|
207
|
+
'TTAC' => 0.7, 'CATT' => 0.7,
|
208
|
+
# A.C mismatches
|
209
|
+
'AATC' => 4.6, 'CTAA' => 4.6,
|
210
|
+
'ACTA' => 14.6, 'ATCA' => 14.6,
|
211
|
+
'CAGC' => 3.7, 'CGAC' => 3.7,
|
212
|
+
'CCGA' => -0.6, 'AGCC' => -0.6,
|
213
|
+
'GACC' => 14.2, 'CCAG' => 14.2,
|
214
|
+
'GCCA' => -3.8, 'ACCG' => -3.8,
|
215
|
+
'TAAC' => 8.0, 'CAAT' => 8.0,
|
216
|
+
'TCAA' => 20.2, 'AACT' => 20.2,
|
217
|
+
# tandem mismatch
|
218
|
+
'GGTT' => 16.3, 'TTGG' => 16.3,
|
219
|
+
'GTTG' => 9.5, 'TGGT' => -6.2,
|
220
|
+
'GTTT' => 16.3, 'TTTG' => 16.3,
|
221
|
+
'GTAT' => -1.7, 'TATG' => -1.7,
|
222
|
+
# single bulge loop
|
223
|
+
'AAAT-T' => -17.5, 'AATT-A' => -44.6, 'AACT-G' => 25.8, 'AAGT-C' => -4.6,
|
224
|
+
'ATAT-T' => 24.7, 'ATTT-A' => -61.8, 'ATCT-G' => -20.0, 'ATGT-C' => 12.9,
|
225
|
+
'ACAT-T' => 14.0, 'ACTT-A' => -15.3, 'ACCT-G' => -91.3, 'ACGT-C' => -7.4,
|
226
|
+
'AGAT-T' => 43.1, 'AGTT-A' => 10.6, 'AGCT-G' => -28.4, 'AGGT-C' => 14.4,
|
227
|
+
'TAAA-T' => 38.5, 'TATA-A' => 56.7, 'TACA-G' => -12.7, 'TAGA-C' => 40.4,
|
228
|
+
'TTAA-T' => -16.0, 'TTTA-A' => -30.1, 'TTCA-G' => 23.2, 'TTGA-C' => 17.5,
|
229
|
+
'TCAA-T' => -3.9, 'TCTA-A' => 30.5, 'TCCA-G' => -48.7, 'TCGA-C' => -7.0,
|
230
|
+
'TGAA-T' => -47.0, 'TGTA-A' => 59.8, 'TGCA-G' => 1.6, 'TGGA-C' => -31.4,
|
231
|
+
'CAAG-T' => -46.6, 'CATG-A' => -25.8, 'CACG-G' => 8.8, 'CAGG-C' => -13.0,
|
232
|
+
'CTAG-T' => -61.7, 'CTTG-A' => -17.0, 'CTCG-G' => -48.1, 'CTGG-C' => -18.8,
|
233
|
+
'CCAG-T' => 13.4, 'CCTG-A' => -24.8, 'CCCG-G' => -9.4, 'CCGG-C' => 24.4,
|
234
|
+
'CGAG-T' => -49.6, 'CGTG-A' => 6.5, 'CGCG-G' => -17.8, 'CGGG-C' => -51.6,
|
235
|
+
'GAAC-T' => -25.2, 'GATC-A' => -35.6, 'GACC-G' => -18.3, 'GAGC-C' => -21.0,
|
236
|
+
'GTAC-T' => -27.0, 'GTTC-A' => -0.6, 'GTCC-G' => -40.0, 'GTGC-C' => -10.0,
|
237
|
+
'GCAC-T' => -12.5, 'GCTC-A' => -16.1, 'GCCC-G' => -1.0, 'GCGC-C' => 42.9,
|
238
|
+
'GGAC-T' => 3.6, 'GGTC-A' => -9.3, 'GGCC-G' => -7.2, 'GGGC-C' => 8.5,
|
239
|
+
# single dangling_end
|
240
|
+
'AA-T' => 2.3, 'TA-T' => -20.0, 'GA-T' => -1.6, 'CA-T' => 3.3,
|
241
|
+
'AC-G' => -17.1, 'TC-G' => -10.9, 'GC-G' => -14.0, 'CC-G' => -12.6,
|
242
|
+
'AG-C' => -10, 'TG-C' => -13.8, 'GG-C' => -10.9, 'CG-C' => -11.9,
|
243
|
+
'AT-A' => -7.6, 'TT-A' => -0.5, 'GT-A' => -15.0, 'CT-A' => -13.0,
|
244
|
+
'AAT-' => -1.1, 'ACT-' => 14.2, 'AGT-' => -13.1, 'ATT-' => -12.6,
|
245
|
+
'TAA-' => -0.8, 'TCA-' => 14.9, 'TGA-' => -3.6, 'TTA-' => 10.4,
|
246
|
+
'GAC-' => -3.9, 'GCC-' => -0.1, 'GGC-' => -11.2, 'GTC-' => -13.1,
|
247
|
+
'CAG-' => -16.5, 'CCG-' => -7.4, 'CGG-' => -10.4, 'CTG-' => -15.0,
|
248
|
+
# long dangling_end
|
249
|
+
'CAAG--' => -5.5, 'CAAAG---' => -8.5, 'CAAAAG----' => -13.5,
|
250
|
+
'TAAA--' => -1.0, 'TAAAA---' => -4.5, 'TAAAAA----' => -6.0,
|
251
|
+
'AAA--T' => -2.5, 'AAAA---T' => -3.5, 'AAAAA----T' => -10.5,
|
252
|
+
'AAG--C' => 0.5, 'AAAG---C' => 1.5, 'AAAAG----C' => -0.5,
|
253
|
+
}
|
254
|
+
|
255
|
+
LONG_BULGE_LOOP_DS = {
|
256
|
+
'2' => -9.35, '3' => -10.0, '4' => -10.32, '5' => -10.64, '6' => -11.28,
|
257
|
+
'7' => -11.93, '8' => -12.57, '9' => -13.22, '10' => -13.86, '11' => -14.15,
|
258
|
+
'12' => -14.51, '13' => -15.00, '14' => -15.48, '15' => -15.65, '16' => -16.12,
|
259
|
+
'17' => -16.26, '18' => -16.77, '19' => -16.80, '20' => -17.09,
|
260
|
+
}
|
261
|
+
|
262
|
+
TANDEM_MISMATCH = {
|
263
|
+
'GT' => ['TT', 'AT', 'TG'],
|
264
|
+
'TT' => ['TG', 'GG'],
|
265
|
+
'TG' => ['GT'],
|
266
|
+
'GG' => ['TT'],
|
267
|
+
'TA' => ['TG'],
|
268
|
+
}
|
269
|
+
|
270
|
+
PERFECT_MATCH = {
|
271
|
+
'A' => 'T',
|
272
|
+
'T' => 'A',
|
273
|
+
'C' => 'G',
|
274
|
+
'G' => 'C',
|
275
|
+
}
|
276
|
+
|
277
|
+
|
278
|
+
end
|
279
|
+
end
|
280
|
+
|
281
|
+
if $0 == __FILE__
|
282
|
+
p Qu::Thermo::DH
|
283
|
+
end
|
data/qu-thermo.gemspec
ADDED
@@ -0,0 +1,23 @@
|
|
1
|
+
# coding: utf-8
|
2
|
+
lib = File.expand_path('../lib', __FILE__)
|
3
|
+
$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
|
4
|
+
require 'qu/thermo/version'
|
5
|
+
|
6
|
+
Gem::Specification.new do |spec|
|
7
|
+
spec.name = "qu-thermo"
|
8
|
+
spec.version = Qu::Thermo::VERSION
|
9
|
+
spec.authors = ["Wubin Qu"]
|
10
|
+
spec.email = ["quwubin@gmail.com"]
|
11
|
+
spec.description = %q{A thermodynamics library for calculating DNA/DNA binding energy}
|
12
|
+
spec.summary = %q{Thermodynamics parameters and calculations}
|
13
|
+
spec.homepage = "https://github.com/quwubin/qu-thermo"
|
14
|
+
spec.license = "MIT"
|
15
|
+
|
16
|
+
spec.files = `git ls-files`.split($/)
|
17
|
+
spec.executables = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
|
18
|
+
spec.test_files = spec.files.grep(%r{^(test|spec|features)/})
|
19
|
+
spec.require_paths = ["lib"]
|
20
|
+
|
21
|
+
spec.add_development_dependency "bundler", "~> 1.3"
|
22
|
+
spec.add_development_dependency "rake"
|
23
|
+
end
|
metadata
ADDED
@@ -0,0 +1,81 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: qu-thermo
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 1.0.0
|
5
|
+
platform: ruby
|
6
|
+
authors:
|
7
|
+
- Wubin Qu
|
8
|
+
autorequire:
|
9
|
+
bindir: bin
|
10
|
+
cert_chain: []
|
11
|
+
date: 2014-04-28 00:00:00.000000000 Z
|
12
|
+
dependencies:
|
13
|
+
- !ruby/object:Gem::Dependency
|
14
|
+
name: bundler
|
15
|
+
requirement: !ruby/object:Gem::Requirement
|
16
|
+
requirements:
|
17
|
+
- - "~>"
|
18
|
+
- !ruby/object:Gem::Version
|
19
|
+
version: '1.3'
|
20
|
+
type: :development
|
21
|
+
prerelease: false
|
22
|
+
version_requirements: !ruby/object:Gem::Requirement
|
23
|
+
requirements:
|
24
|
+
- - "~>"
|
25
|
+
- !ruby/object:Gem::Version
|
26
|
+
version: '1.3'
|
27
|
+
- !ruby/object:Gem::Dependency
|
28
|
+
name: rake
|
29
|
+
requirement: !ruby/object:Gem::Requirement
|
30
|
+
requirements:
|
31
|
+
- - ">="
|
32
|
+
- !ruby/object:Gem::Version
|
33
|
+
version: '0'
|
34
|
+
type: :development
|
35
|
+
prerelease: false
|
36
|
+
version_requirements: !ruby/object:Gem::Requirement
|
37
|
+
requirements:
|
38
|
+
- - ">="
|
39
|
+
- !ruby/object:Gem::Version
|
40
|
+
version: '0'
|
41
|
+
description: A thermodynamics library for calculating DNA/DNA binding energy
|
42
|
+
email:
|
43
|
+
- quwubin@gmail.com
|
44
|
+
executables: []
|
45
|
+
extensions: []
|
46
|
+
extra_rdoc_files: []
|
47
|
+
files:
|
48
|
+
- ".gitignore"
|
49
|
+
- Gemfile
|
50
|
+
- LICENSE.txt
|
51
|
+
- README.md
|
52
|
+
- Rakefile
|
53
|
+
- lib/qu/thermo.rb
|
54
|
+
- lib/qu/thermo/parameters.rb
|
55
|
+
- lib/qu/thermo/version.rb
|
56
|
+
- qu-thermo.gemspec
|
57
|
+
homepage: https://github.com/quwubin/qu-thermo
|
58
|
+
licenses:
|
59
|
+
- MIT
|
60
|
+
metadata: {}
|
61
|
+
post_install_message:
|
62
|
+
rdoc_options: []
|
63
|
+
require_paths:
|
64
|
+
- lib
|
65
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
66
|
+
requirements:
|
67
|
+
- - ">="
|
68
|
+
- !ruby/object:Gem::Version
|
69
|
+
version: '0'
|
70
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
71
|
+
requirements:
|
72
|
+
- - ">="
|
73
|
+
- !ruby/object:Gem::Version
|
74
|
+
version: '0'
|
75
|
+
requirements: []
|
76
|
+
rubyforge_project:
|
77
|
+
rubygems_version: 2.2.0
|
78
|
+
signing_key:
|
79
|
+
specification_version: 4
|
80
|
+
summary: Thermodynamics parameters and calculations
|
81
|
+
test_files: []
|