2020-11-14

Unpack

安裝可以使用conda 進(jìn)行安裝

下面的所有程序需要在power shell下運(yùn)行

下面的如何運(yùn)行等等教程什么的

https://www.cnblogs.com/lsdb/p/9531338.html

Conda 安裝教程

http://www.reibang.com/p/edaa744ea47d

miniconda官網(wǎng)：https://conda.io/miniconda.html

下面的這些可以參考 windows10下安裝conda?http://www.reibang.com/p/920a6e18cfd6

安裝python3.7的minconda；

就是下載下來一步一步安裝即可规揪。

添加環(huán)境變量

換源

conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/

conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge

conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2/

安裝openssl

在執(zhí)行conda upgrade --all時(shí)，報(bào)SSLError，需要安裝openssl

下載地址：

下載后直接安裝就行

https://slproweb.com/products/Win32OpenSSL.html

試運(yùn)行

在shell里面運(yùn)行運(yùn)行程序

#下面的這個(gè)就是如何使用conda對nupack進(jìn)行設(shè)計(jì)的

conda install -c beliveau-lab nupack

=================================================================================

如果只是在網(wǎng)頁是上使用晴玖，可以http://www.nupack.org/partition/new

復(fù)雜分析

分析相互作用的核酸鏈復(fù)合物的平衡堿基配對特性

pfunc: 計(jì)算分區(qū)函數(shù)

在集合Γ'上計(jì)算分區(qū)函數(shù)Q（φ）

pfunc [-Ttemperature] [-multi] [-pseudo] [-materialparameters][-danglestreatment]prefix

#下面就是運(yùn)行的程序

(base) zhangjiandeMacBook-Pro:CleaveLand4-master zhangjian$ pfunc

No input file specified.

Requesting input manually.

% NUPACK 3.2.2

% Program: pfunc

% Start time: Wed Nov 25 10:46:58 2020

% Command: pfunc

Enter sequence:

單鏈計(jì)算

如果只是單條鏈沒有其他什么參數(shù)可以直接在終端里面輸入序列；

下面的就是對GGGCUGUUUUUCUCGCUGACUUUCAGCCCCAAACAAAAAAUGUCAGCA這條鏈進(jìn)行計(jì)算侍芝；

(base) zhangjiandeMacBook-Pro:CleaveLand4-master zhangjian$ pfunc

No input file specified.

Requesting input manually.

% NUPACK 3.2.2

% Program: pfunc

% Start time: Wed Nov 25 10:46:58 2020

% Command: pfunc

Enter sequence: GGGCUGUUUUUCUCGCUGACUUUCAGCCCCAAACAAAAAAUGUCAGCA

% Sequence:? GGGCUGUUUUUCUCGCUGACUUUCAGCCCCAAACAAAAAAUGUCAGCA

% v(pi): 1

% Parameters: RNA, 1995

#這里是說明序列的種類是什么rna or dna

% Dangles setting: 1

#這個(gè)是一個(gè)什么能量箱锐，是一個(gè)專有名詞比勉。（不了解????????）

% Temperature (C): 37.0

#這個(gè)是設(shè)置的溫度

% Sodium concentration: 1.0000 M

#這個(gè)是設(shè)置的鈉濃度

% Magnesium concentration: 0.0000 M

#這個(gè)是設(shè)置鎂離子濃度

% Free energy (kcal/mol) and partition function:

-1.13589149e+01

1.00956434994643e+08

#這個(gè)是計(jì)算出來的自由能和一個(gè)叫什么分離函數(shù)什么的（專有名詞）

上面的這個(gè)就可以對應(yīng)到下面這個(gè)圖的參數(shù)，如果上面的沒有就不用設(shè)置的驹止，保持默認(rèn)就可以了

多條鏈計(jì)算

計(jì)算在23℃下由四個(gè)DNA鏈組成的復(fù)合物的分區(qū)函數(shù)浩聋，其中兩個(gè)是無法區(qū)分的。

需要準(zhǔn)備的輸入文件如下

#第一行是說明有幾種序列

#第二行到第四行為3中序列的具體參數(shù)

#第五行為每個(gè)序列的重復(fù)情況臊恋，這里就是第一條鏈重復(fù)一次衣洁，第二條鏈重復(fù)兩次，第三條鏈重復(fù)一次抖仅。

AGTCTAGGATTCGGCGTGGGTTAA

TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG

AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG

1 2 2 3

這里可以使用atom創(chuàng)建prefix.in文件

atom下載地址https://atom.io/

例如下圖所示坊夫，創(chuàng)建的prefix.in文件

#由于項(xiàng)目這里是對多條鏈進(jìn)行計(jì)算，因此這里就需要設(shè)置-multi參數(shù)撤卢，這個(gè)參數(shù)就是多條鏈計(jì)算參數(shù)环凿。

Command: pfunc -T 23 -multi -material dna /Users/zhangjian/Desktop/prefix

% Sequence:? AGTCTAGGATTCGGCGTGGGTTAA+TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG+TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG+AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG

% v(pi): 1

% Parameters: DNA, 1998

% Dangles setting: 1

% Temperature (C): 23.0

% Sodium concentration: 1.0000 M

% Magnesium concentration: 0.0000 M

% Free energy (kcal/mol) and partition function:

-1.21970714e+02

1.02444390480969e+90

pairs: calculate base-pairing observables

計(jì)算堿基配對可觀察值（這個(gè)翻譯對不對不一定）

Computes pair probabilities p(i n· j m) for the complex corresponding to the speci?ed strand ordering π. When -multi is selected, also computes the expected number of base pairs E(i { A } · j { B } ).

-cutoff cutoffvalue #僅等于或大于cutoffvalue（默認(rèn)值：0.001）的概率和期望值保存在輸出文件中

#還使用這個(gè)文件當(dāng)做輸入文件

AGTCTAGGATTCGGCGTGGGTTAA

TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG

AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG

1 2 2 3

#下面就是這個(gè)重程序運(yùn)行的情況

(base) zhangjiandeMacBook-Pro:CleaveLand4-master zhangjian$ pairs -T 23 -multi -material dna -cutoff /Users/zhangjian/Desktop/prefix

Invalid cutoff

#運(yùn)行結(jié)果就在運(yùn)行目錄下面的一個(gè)prefix.mfe文件

文件具體內(nèi)容

這些稀奇古怪的文件格式，都可以使用文本編輯器進(jìn)行打開放吩，win下面可以就打開方式選擇文本編輯器

% NUPACK 3.2.2

% Program: mfe

% Start time: Tue Nov 24 23:22:27 2020

% Command: mfe -T 23 -multi -material dna /Users/zhangjian/Desktop/prefix

% Sequence:? AGTCTAGGATTCGGCGTGGGTTAA+TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG+TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG+AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG

% v(pi): 1

% Parameters: DNA, 1998

% Dangles setting: 1

% Temperature (C): 23.0

% Sodium concentration: 1.0000 M

% Magnesium concentration: 0.0000 M

% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %

168

-119.494

.(((((((((((((((((((((((+))))))))))))))))))))))).((((((((((((((((((((((((+..(((((((((((((((((((((....((....)).............+.)))))))))))))))))))))..))))))))))))))))))))))))

2 47

3 46

4 45

5 44

6 43

7 42

8 41

9 40

10 39

11 38

12 37

13 36

14 35

15 34

16 33

17 32

18 31

19 30

20 29

21 28

22 27

23 26

24 25

49 168

50 167

51 166

52 165

53 164

54 163

55 162

56 161

57 160

58 159

59 158

60 157

61 156

62 155

63 154

64 153

65 152

66 151

67 150

68 149

69 148

70 147

71 146

72 145

75 142

76 141

77 140

78 139

79 138

80 137

81 136

82 135

83 134

84 133

85 132

86 131

87 130

88 129

89 128

90 127

91 126

92 125

93 124

94 123

95 122

100 107

101 106

% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %

mfe: find the minimum free energy (MFE) secondary structure(s)

找到具有最小自由能的二級結(jié)構(gòu)

確定在復(fù)合體Γ上的序列φ的最小自由能二級結(jié)構(gòu)sMFE（φ）智听。如果選擇了簡并標(biāo)記，則確定所有具有最小自由能的二級結(jié)構(gòu)渡紫。否則到推，僅返回一個(gè)MFE結(jié)構(gòu)

(base) zhangjiandeMacBook-Pro:CleaveLand4-master zhangjian$ mfe -T 23 -multi -material dna -cutoff /Users/zhangjian/Desktop/prefix

Invalid cutoff

#這里輸出的是沒有有效的結(jié)果，可能是因?yàn)樾睦锊⒉贿m合惕澎，同時(shí)如果沒有有效的結(jié)果莉测，返回的就是MFE的結(jié)果。

subopt：在MFE的指定自由能隙內(nèi)找到所有二級結(jié)構(gòu)

subopt -T 23 -multi -material dna -cutoff /Users/zhangjian/Desktop/prefix

Invalid cutoff

如果有輸出的話就是一個(gè)prefix.subopt的文件唧喉，和上面的MFE輸出的還差不多捣卤。

count：計(jì)算集合中二級結(jié)構(gòu)的數(shù)量

計(jì)算復(fù)合體集合中二級結(jié)構(gòu)的數(shù)量忍抽，|Γ|，將所有鏈視為不同

#比如計(jì)算下面序列的所有二級序列總和

(base) zhangjiandeMacBook-Pro:CleaveLand4-master zhangjian$ count -multi -material dna /Users/zhangjian/Desktop/prefix

% NUPACK 3.2.2

% Program: count

% Start time: Wed Nov 25 11:51:58 2020

% Command: count -multi -material dna /Users/zhangjian/Desktop/prefix

% Sequence:? AGTCTAGGATTCGGCGTGGGTTAA+TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG+TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG+AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG

% v(pi): 1

% Parameters: DNA, 1998

% Dangles setting: 1

% Temperature (C): 37.0

% Sodium concentration: 1.0000 M

% Magnesium concentration: 0.0000 M

% Total number of secondary structures:

1.88454748279349e+39

Energy：計(jì)算二級結(jié)構(gòu)的自由能

輸入對應(yīng)的結(jié)構(gòu)加上序列信息腌零，對序列的二級結(jié)構(gòu)進(jìn)行換算

這里如果不知道怎么用點(diǎn)括號法表示核酸二級結(jié)構(gòu)

可以把RNA序列放到http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi

下面就是用一段序列生成的函數(shù)二級結(jié)構(gòu)什么的

dna的可以使用Mfold

(base) zhangjiandeMacBook-Pro:CleaveLand4-master zhangjian$ energy -T 23 -material dna /Users/zhangjian/Desktop/prefix

% NUPACK 3.2.2

% Program: energy

% Start time: Wed Nov 25 11:57:12 2020

% Command: energy -T 23 -material dna /Users/zhangjian/Desktop/prefix

% NUPACK 3.2.2

% Program: energy

% Start time: Wed Nov 25 11:57:12 2020

% Command: energy -T 23 -material dna /Users/zhangjian/Desktop/prefix

% Sequence: GGUACUUAGGGUGCUUCAGCACCAGAAGUUGUAUGCUAAAUUUGCUAAGUGCGAGUUCUGGUUGACUUCAGUGGCAUUCUUGGGGCA

% Structure: .((.((.((((((((.(((((((((((.((((((((.......))...)))))).)))))).)).))...).)))))))).)).)).

% v(pi): 1

% Parameters: DNA, 1998

% Dangles setting: 1

% Temperature (C): 23.0

% Sodium concentration: 1.0000 M

% Magnesium concentration: 0.0000 M

% Energy (kcal/mol):

-8.01379493793326

prob: calculate the equilibrium probability of a secondary structure

計(jì)算二級結(jié)構(gòu)的平衡概率

計(jì)算平衡概率p（φ梯找，s），該序列在復(fù)合體Γ'內(nèi)采用二級結(jié)構(gòu)

輸入文件是和energy計(jì)算一樣的

(base) zhangjiandeMacBook-Pro:CleaveLand4-master zhangjian$ prob -T 23 -material dna /Users/zhangjian/Desktop/prefix

% NUPACK 3.2.2

% Program: prob

% Start time: Wed Nov 25 14:49:32 2020

% Command: prob -T 23 -material dna /Users/zhangjian/Desktop/prefix

% Sequence:? GGUACUUAGGGUGCUUCAGCACCAGAAGUUGUAUGCUAAAUUUGCUAAGUGCGAGUUCUGGUUGACUUCAGUGGCAUUCUUGGGGCA

% Structure: .((.((.((((((((.(((((((((((.((((((((.......))...)))))).)))))).)).))...).)))))))).)).)).

% v(pi): 1

% Parameters: DNA, 1998

% Dangles setting: 1

% Temperature (C): 23.0

% Sodium concentration: 1.0000 M

% Magnesium concentration: 0.0000 M

% Probability:

3.175e-08

試管分析

分析相互作用的核酸鏈的試管的平衡堿基配對特性和濃度

complexes: calculate the partition function and equilibrium base-pairing properties for each com-plex in a test tube

絡(luò)合物：計(jì)算試管中每個(gè)絡(luò)合物的分配函數(shù)和平衡堿基配對屬性

對于鏈Ψ0的集合益涧，計(jì)算每個(gè)復(fù)合物j∈Ψ的分區(qū)函數(shù)Qj，對應(yīng)于最多Lmax個(gè)鏈的所有復(fù)合物驯鳖∠醒可以通過命令行標(biāo)志來指定重要的附加功能。復(fù)合體的輸出可以用作可執(zhí)行文件的輸入浅辙。

輸入文件示例

prefix.in文件如下

%第一行為序列種數(shù)

%第二行到第四行為3個(gè)序列的具體堿基序列

%第五行為最大復(fù)數(shù)Lmax（這里不是很清楚）

AGTCTAGGATTCGGCGTGGGTTAA

TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG

AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG

prefix.list文件如下

%1到|Ψ0|范圍內(nèi)的L整數(shù)列表扭弧，表示復(fù)合物的鏈順序

%下面的每一個(gè)數(shù)字表示上面的一條鏈如1就是“AGTCTAGGATTCGGCGTGGGTTAA”

%整合上面的文件中的4就是一個(gè)有4種的不同組合。

1 2 2 3 3

1 2 3 2 3

2 3 2 3 2

1 2 2 2 3 3

運(yùn)行實(shí)例

#這里的-T 后面要加上溫度记舆，-material 要指明計(jì)算的核酸種類 -pairs 是按照可執(zhí)行對計(jì)算堿基對可觀察值 -mfe? 計(jì)算每個(gè)復(fù)合體的所有MFE結(jié)構(gòu)

#-cutoff cutoffvalue 在選擇pairs flags時(shí)生成的輸出文件中僅保存等于或大于cutoffvalue（默認(rèn)值：0.001）的概率和期望值

#-timeonly 要多少時(shí)間完成計(jì)算

#-v3.0 以3.0版本運(yùn)行程序

#-quiet 安靜的運(yùn)行程序鸽捻，就是不會(huì)在屏幕上出現(xiàn)太多東西

(base) zhangjiandeMacBook-Pro:~ zhangjian$ complexes? -T 23 -material dna -pairs -mfe -degenerate? /Users/zhangjian/Desktop/prefix concentrations -pairs /Users/zhangjian/Desktop/prefix

Relative to NUPACK 3.0, the following changes were introduced to

the complexes executable:

? -ordered is on by default

? output files .cx and .cx-epairs are not written

? the comment lines in .ocx-epairs and .ocx-mfe employ updated terminology

Use the -v3.0 option to revert to NUPACK 3.0 behavior.

Permutation generation complete.

Starting partition function calculations.

Rough time estimate for calculation: 182.77 seconds

Status: Set 1 / 37: nPerms (1)? 1 / 48

Status: Set 2 / 37: nPerms (1)? 2 / 48

Status: Set 3 / 37: nPerms (1)? 3 / 48

Status: Set 4 / 37: nPerms (1)? 4 / 48

Status: Set 5 / 37: nPerms (1)? 5 / 48

Status: Set 6 / 37: nPerms (1)? 6 / 48

Status: Set 7 / 37: nPerms (1)? 7 / 48

Status: Set 8 / 37: nPerms (1)? 8 / 48

Status: Set 9 / 37: nPerms (1)? 9 / 48

Status: Set 10 / 37: nPerms (1)? 10 / 48

Status: Set 11 / 37: nPerms (1)? 11 / 48

Status: Set 12 / 37: nPerms (1)? 12 / 48

Status: Set 13 / 37: nPerms (1)? 13 / 48

Status: Set 14 / 37: nPerms (2)? 14 / 48

Status: Set 15 / 37: nPerms (1)? 16 / 48

Status: Set 16 / 37: nPerms (1)? 17 / 48

Status: Set 17 / 37: nPerms (1)? 18 / 48

Status: Set 18 / 37: nPerms (1)? 19 / 48

Status: Set 19 / 37: nPerms (1)? 20 / 48

Status: Set 20 / 37: nPerms (1)? 21 / 48

Status: Set 21 / 37: nPerms (1)? 22 / 48

Status: Set 22 / 37: nPerms (1)? 23 / 48

Status: Set 23 / 37: nPerms (2)? 24 / 48

Status: Set 24 / 37: nPerms (3)? 26 / 48

Status: Set 25 / 37: nPerms (2)? 29 / 48

Status: Set 26 / 37: nPerms (1)? 31 / 48

Status: Set 27 / 37: nPerms (3)? 32 / 48

Status: Set 28 / 37: nPerms (3)? 35 / 48

Status: Set 29 / 37: nPerms (1)? 38 / 48

Status: Set 30 / 37: nPerms (1)? 39 / 48

Status: Set 31 / 37: nPerms (1)? 40 / 48

Status: Set 32 / 37: nPerms (2)? 41 / 48

Status: Set 33 / 37: nPerms (1)? 43 / 48

Status: Set 34 / 37: nPerms (1)? 44 / 48

Status: Set 35 / 37: nPerms (2)? 45 / 48

Status: Set 36 / 37: nPerms (1)? 47 / 48

Status: Set 37 / 37: nPerms (1)? 48 / 48

Total number of terms calculated: 48 (48)

Calculation finished on: Wed Nov 25 15:08:33 2020

生成的文件

prefix.ocx文件的內(nèi)容(節(jié)選）

% NUPACK 3.2.2

% Program: complexes

% Start time: Wed Nov 25 15:08:18 2020 PST

% Command: complexes -T 23 -material dna -pairs -mfe -degenerate -pairs /Users/zhangjian/Desktop/prefix concentrations /Users/zhangjian/Desktop/prefix

% Maximum complex size to enumerate: 4

% Number of complexes from enumeration: 44

% Additional complexes from .list file: 4

% Total number of complexes: 48

% Parameters: DNA, 1998

% Dangles setting: 1

% Temperature (C): 23.0

% Sodium concentration: 1.0000 M

% Magnesium concentration: 0.0000 M

% Do not change the comments below this line, as they may be read by other programs!

% Number of strands: 3

% id sequence

%? 1 AGTCTAGGATTCGGCGTGGGTTAA

%? 2 TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG

%? 3 AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG

% T = 23.0

1 1 1 0 0 -7.87585320e-01

2 1 0 1 0 -2.77229511e+01

3 1 0 0 1 -2.80354395e+01

4 1 2 0 0 -1.07109347e+01

5 1 1 1 0 -4.15225790e+01

6 1 1 0 1 -3.42779194e+01

7 1 0 2 0 -5.88918294e+01

8 1 0 1 1 -5.91190488e+01

9 1 0 0 2 -6.04508699e+01

10 1 3 0 0 -1.86535120e+01

11 1 2 1 0 -5.21814376e+01

12 1 2 0 1 -4.46710992e+01

13 1 1 2 0 -7.44330886e+01

14 1 1 1 1 -8.17640179e+01

14 2 1 1 1 -7.10190272e+01

15 1 1 0 2 -6.76235463e+01

16 1 0 3 0 -9.00673131e+01

17 1 0 2 1 -9.04005684e+01

18 1 0 1 2 -9.19265778e+01

19 1 0 0 3 -9.22563355e+01

20 1 4 0 0 -2.88102348e+01

21 1 3 1 0 -6.00477161e+01

22 1 3 0 1 -5.27376513e+01

23 1 2 2 0 -8.53462065e+01

23 2 2 2 0 -9.28574307e+01

24 1 2 1 1 -8.58158470e+01

24 2 2 1 1 -8.16781270e+01

24 3 2 1 1 -9.21079593e+01

refix.ocx-epairs文件內(nèi)容(節(jié)選）

% NUPACK 3.2.2

% Program: complexes

% Start time: Wed Nov 25 15:08:18 2020 PST

% Command: complexes -T 23 -material dna -pairs -mfe -degenerate -pairs /Users/zhangjian/Desktop/prefix concentrations /Users/zhangjian/Desktop/prefix

% Maximum complex size to enumerate: 4

% Minimum output pair probability: 0.001

% Number of complexes from enumeration: 44

% Additional complexes from .list file: 4

% Total number of complexes: 48

% Parameters: DNA, 1998

% Dangles setting: 1

% Temperature (C): 23.0

% Sodium concentration: 1.0000 M

% Magnesium concentration: 0.0000 M

% Do not change the comments below this line, as they may be read by other programs!

% Number of strands: 3

% id sequence

%? 1 AGTCTAGGATTCGGCGTGGGTTAA

%? 2 TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG

%? 3 AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG

% T = 23.0

% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %

% composition1-ordering1

120

1 5 2.707e-03

1 10 4.089e-03

1 11 1.026e-02

1 17 1.924e-03

1 21 3.609e-03

1 22 2.361e-03

2 10 8.574e-03

2 12 1.171e-02

2 15 4.715e-02

3 8 2.373e-03

3 9 3.436e-02

3 14 3.927e-02

3 19 2.986e-03

4 8 5.055e-02

4 13 3.333e-02

4 14 1.877e-02

4 16 7.577e-03

4 18 1.816e-02

4 19 8.623e-02

4 20 1.839e-02

5 9 2.048e-03

5 13 5.158e-03

5 18 7.197e-02

5 19 8.534e-03

5 23 5.228e-03

prefix.ocx-key?文件的內(nèi)容(節(jié)選）

% NUPACK 3.2.2

% Program: complexes

% Start time: Wed Nov 25 15:08:18 2020 PST

% Command: complexes -T 23 -material dna -pairs -mfe -degenerate -pairs /Users/zhangjian/Desktop/prefix concentrations /Users/zhangjian/Desktop/prefix

% Maximum complex size to enumerate: 4

% Number of complexes from enumeration: 44

% Additional complexes from .list file: 4

% Total number of complexes: 48

% Parameters: DNA, 1998

% Dangles setting: 1

% Temperature (C): 23.0

% Sodium concentration: 1.0000 M

% Magnesium concentration: 0.0000 M

% Do not change the comments below this line, as they may be read by other programs!

% Number of strands: 3

% id sequence

%? 1 AGTCTAGGATTCGGCGTGGGTTAA

%? 2 TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG

%? 3 AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG

% T = 23.0

1 1 1

2 1 2

3 1 3

4 1 1 1

5 1 1 2

6 1 1 3

7 1 2 2

8 1 2 3

9 1 3 3

10 1 1 1 1

11 1 1 1 2

12 1 1 1 3

13 1 1 2 2

14 1 1 2 3

14 2 1 3 2

15 1 1 3 3

16 1 2 2 2

17 1 2 2 3

18 1 2 3 3

19 1 3 3 3

20 1 1 1 1 1

prefix.ocx-mfe?文件的內(nèi)容(節(jié)選）

% NUPACK 3.2.2

% Program: complexes

% Start time: Wed Nov 25 15:08:18 2020 PST

% Command: complexes -T 23 -material dna -pairs -mfe -degenerate -pairs /Users/zhangjian/Desktop/prefix concentrations /Users/zhangjian/Desktop/prefix

% Maximum complex size to enumerate: 4

% Number of complexes from enumeration: 44

% Additional complexes from .list file: 4

% Total number of complexes: 48

% Parameters: DNA, 1998

% Dangles setting: 1

% Temperature (C): 23.0

% Sodium concentration: 1.0000 M

% Magnesium concentration: 0.0000 M

% Do not change the comments below this line, as they may be read by other programs!

% Number of strands: 3

% id sequence

%? 1 AGTCTAGGATTCGGCGTGGGTTAA

%? 2 TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG

%? 3 AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG

% T = 23.0

% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %

% composition1-ordering1

0.00000000e+00

........................

% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %

% composition2-ordering1

-2.75828841e+01

......((((((((((((((((((......))))))))))))))))))

7 48

8 47

9 46

10 45

11 44

12 43

13 42

14 41

15 40

16 39

17 38

18 37

19 36

20 35

21 34

22 33

23 32

24 31

% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %

% composition3-ordering1

-2.77667355e+01

((((((((((((((((((......))))))))))))))))))......

1 42

2 41

3 40

4 39

5 38

6 37

7 36

8 35

9 34

10 33

11 32

12 31

13 30

14 29

15 28

16 27

17 26

18 25

% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %

% composition4-ordering1

-1.04023100e+01

...........((.((........+...........)).))........

12 40

13 39

15 37

16 36

% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %

prefix.ocx-ppairs?文件的內(nèi)容(節(jié)選）

% NUPACK 3.2.2

% Program: complexes

% Start time: Wed Nov 25 15:08:18 2020 PST

% Command: complexes -T 23 -material dna -pairs -mfe -degenerate -pairs /Users/zhangjian/Desktop/prefix concentrations /Users/zhangjian/Desktop/prefix

% Maximum complex size to enumerate: 4

% Minimum output pair probability: 0.001

% Number of complexes from enumeration: 44

% Additional complexes from .list file: 4

% Total number of complexes: 48

% Parameters: DNA, 1998

% Dangles setting: 1

% Temperature (C): 23.0

% Sodium concentration: 1.0000 M

% Magnesium concentration: 0.0000 M

% Do not change the comments below this line, as they may be read by other programs!

% Number of strands: 3

% id sequence

%? 1 AGTCTAGGATTCGGCGTGGGTTAA

%? 2 TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG

%? 3 AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG

% T = 23.0

% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %

% composition1-ordering1

1 5 2.707e-03

1 10 4.089e-03

1 11 1.026e-02

1 17 1.924e-03

1 21 3.609e-03

1 22 2.361e-03

2 10 8.574e-03

2 12 1.171e-02

2 15 4.715e-02

3 8 2.373e-03

3 9 3.436e-02

3 14 3.927e-02

3 19 2.986e-03

4 8 5.055e-02

4 13 3.333e-02

4 14 1.877e-02

4 16 7.577e-03

4 18 1.816e-02

4 19 8.623e-02

4 20 1.839e-02

5 9 2.048e-03

5 13 5.158e-03

5 18 7.197e-02

5 19 8.534e-03

5 23 5.228e-03

6 10 4.368e-02

6 11 2.266e-02

6 17 1.248e-01

6 21 2.386e-03

6 22 1.121e-02

7 12 3.150e-02

7 15 1.720e-02

7 21 2.649e-03

8 12 5.961e-03

8 15 1.237e-01

9 17 1.644e-02

9 21 1.232e-02

9 22 5.647e-03

10 16 1.232e-02

10 20 9.301e-03

10 23 2.961e-03

10 24 2.578e-02

11 19 7.937e-03

11 23 2.459e-02

11 24 1.158e-03

12 16 9.936e-03

12 18 1.263e-01

12 19 2.621e-02

12 20 1.554e-02

13 17 2.650e-02

13 21 4.834e-03

14 21 6.112e-03

15 19 2.169e-02

15 20 8.830e-02

17 23 4.451e-03

17 24 1.161e-03

1 25 9.751e-01

2 25 9.318e-01

3 25 9.195e-01

4 25 7.670e-01

5 25 9.033e-01

6 25 7.953e-01

7 25 9.470e-01

8 25 8.165e-01

9 25 9.292e-01

10 25 8.923e-01

11 25 9.313e-01

12 25 7.728e-01

13 25 9.298e-01

14 25 9.350e-01

15 25 7.020e-01

16 25 9.695e-01

17 25 8.236e-01

18 25 7.827e-01

19 25 8.461e-01

20 25 8.668e-01

21 25 9.671e-01

22 25 9.795e-01

23 25 9.625e-01

24 25 9.709e-01

% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %

concentrations: calculate the equilibrium concentration for each complex in a test tube

計(jì)算試管中每種復(fù)合物的平衡濃度

給定用戶指定的每種鏈物種的濃度，計(jì)算稀溶液（例如試管）中每種復(fù)雜物種或堿基對的平衡濃度（Dirks et al泽腮。御蒲，2007）。分區(qū)函數(shù)信息是從由可執(zhí)行復(fù)合體生成的輸出文件中讀取的诊赊。

要輸入的文件

prefix.ocx文件來自上面的文件計(jì)算而來

prefix.con文件來自上面的文件計(jì)算而來

%下面就prefix.con文件的內(nèi)容厚满，因?yàn)樯厦媸侨龡l序列因此就指定三個(gè)摩爾濃度

1 1e-6

2 1e-5

3 1e-8

(base) zhangjiandeMacBook-Pro:~ zhangjian$ concentrations -pairs /Users/zhangjian/Desktop/prefix -sort 0? /Users/zhangjian/Desktop/prefix

Relative to NUPACK 3.0, the following change was introduced to the

concentrations executable: the -ordered option is on by default.

Use the -v3.0 option to revert to NUPACK 3.0 behavior.

Error in conservation of mass: #這里報(bào)的信息是摩爾質(zhì)量不失衡????????

? 7.842022e-09 Molar

? 1.624964e-08 Molar

? 1.557208e-08 Molar

Free energy = -1.825048e+02 kcal/litre of solution

Elapsed time: 0 seconds.

#-pairs 就是要指定輸入文件的位置

#-sort? 指定排序方法

下面是prefix.eq文件的內(nèi)容

% NUPACK 3.2.2

% This is /Users/zhangjian/Desktop/prefix.eq, an output file generated for a "concentrations"

% calculation of equilibrium concentrations.

% For information on contents, see NUPACK manual.

% Program: concentrations

% Start time: Wed Nov 25 16:05:26 2020 PST

% Command: concentrations -pairs -sort 0 /Users/zhangjian/Desktop/prefix /Users/zhangjian/Desktop/prefix

% Initial monomer concentrations:

%? 1: 1.000000e+00 Molar

%? 2: 2.000000e+00 Molar

%? 3: 3.000000e+00 Molar

% Following is the header from the input file (/Users/zhangjian/Desktop/prefix.ocx):

% NUPACK 3.2.2

% Program: complexes

% Start time: Wed Nov 25 15:08:18 2020 PST

% Command: complexes -T 23 -material dna -pairs -mfe -degenerate -pairs /Users/zhangjian/Desktop/prefix concentrations /Users/zhangjian/Desktop/prefix

% Maximum complex size to enumerate: 4

% Number of complexes from enumeration: 44

% Additional complexes from .list file: 4

% Total number of complexes: 48

% Parameters: DNA, 1998

% Dangles setting: 1

% Temperature (C): 23.0

% Sodium concentration: 1.0000 M

% Magnesium concentration: 0.0000 M

% Do not change the comments below this line, as they may be read by other programs!

% Number of strands: 3

% id sequence

%? 1 AGTCTAGGATTCGGCGTGGGTTAA

%? 2 TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG

%? 3 AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG

% T = 23.0

1 1 1 0 0 -7.875853e-01 2.616270e-08

2 1 0 1 0 -2.772295e+01 1.253223e-10

3 1 0 0 1 -2.803544e+01 5.793549e-02

4 1 2 0 0 -1.071093e+01 6.823000e-11

5 1 1 1 0 -4.152258e+01 2.370779e-10

6 1 1 0 1 -3.427792e+01 2.903177e-07

7 1 0 2 0 -5.889183e+01 9.902608e-20

8 1 0 1 1 -5.911905e+01 3.960408e-11

9 1 0 0 2 -6.045087e+01 1.034883e-01

10 1 3 0 0 -1.865351e+01 6.144997e-15

11 1 2 1 0 -5.218144e+01 2.157576e-12

12 1 2 0 1 -4.467110e+01 1.682233e-09

13 1 1 2 0 -7.443309e+01 3.613103e-18

14 1 1 1 1 -8.176402e+01 2.524536e-04

下面是prefix.eq文件的內(nèi)容

% NUPACK 3.2.2

% This is /Users/zhangjian/Desktop/prefix.fpairs, an output file generated for a "concentrations"

% calculation of base pair fractions.

% For information on contents, see NUPACK manual.

% Program: concentrations

% Start time: Wed Nov 25 16:05:26 2020 PST

% Command: concentrations -pairs -sort 0 /Users/zhangjian/Desktop/prefix /Users/zhangjian/Desktop/prefix

% Minimum output pair fraction: 0.001

% Initial monomer concentrations:

%? 1: 1.000000e+00 Molar

%? 2: 2.000000e+00 Molar

%? 3: 3.000000e+00 Molar

% Following is the header from the input file (/Users/zhangjian/Desktop/prefix.ocx):

% NUPACK 3.2.2

% Program: complexes

% Start time: Wed Nov 25 15:08:18 2020 PST

% Command: complexes -T 23 -material dna -pairs -mfe -degenerate -pairs /Users/zhangjian/Desktop/prefix concentrations /Users/zhangjian/Desktop/prefix

% Maximum complex size to enumerate: 4

% Number of complexes from enumeration: 44

% Additional complexes from .list file: 4

% Total number of complexes: 48

% Parameters: DNA, 1998

% Dangles setting: 1

% Temperature (C): 23.0

% Sodium concentration: 1.0000 M

% Magnesium concentration: 0.0000 M

% Do not change the comments below this line, as they may be read by other programs!

% Number of strands: 3

% id sequence

%? 1 AGTCTAGGATTCGGCGTGGGTTAA

%? 2 TTAACCCACGCCGAATCCTAGACTCAAAGTAGTCTAGGATTCGGCGTG

%? 3 AGTCTAGGATTCGGCGTGGGTTAACACGCCGAATCCTAGACTACTTTG

% T = 23.0

120

1 48 4.835637e-01

1 121 5.161056e-01

2 47 9.897167e-01

2 121 9.751942e-03

3 46 9.909160e-01

3 121 8.621663e-03

4 45 9.985135e-01

4 121 1.048448e-03

5 44 9.963146e-01

5 121 3.198827e-03

6 43 9.964146e-01

6 121 3.120022e-03

7 42 9.991132e-01

8 41 9.991135e-01

9 40 9.977139e-01

9 121 1.825688e-03

10 39 9.965146e-01

10 121 3.015618e-03

11 38 9.981139e-01

11 121 1.434768e-03

12 37 9.993132e-01

13 36 9.994132e-01

14 35 9.994132e-01

15 34 9.995132e-01

16 33 9.994132e-01

17 32 9.990132e-01

18 31 9.992132e-01

19 30 9.993132e-01

distributions

在一個(gè)小盒子中計(jì)算幾個(gè)復(fù)合物的平衡總體分布和期望值

給定用戶定義的每種鏈種類的種群，可執(zhí)行文件分布為包含少量鏈的盒子計(jì)算分區(qū)函數(shù)Qbox（Dirks等碧磅，2007）碘箍。這用于計(jì)算每種復(fù)合物種群的期望值和概率分布。分區(qū)功能信息是從由可執(zhí)行復(fù)合體生成的輸出文件中讀取的

輸入文件

%第一到底三行為123三條序列分別對應(yīng)的指定每個(gè)鏈種i∈Ψ0的總鏈總數(shù)m0i

%最后一行為? 文件的最后一行包含以升為單位的盒子的體積鲸郊。這可以用科學(xué)記數(shù)法輸入

1 6

2 7

3 5

1.4e-18

distributions

(base) zhangjiandeMacBook-Pro:~ zhangjian$ distributions -maxstates 1e8? -writestates -sort 1? /Users/zhangjian/Desktop/prefix

Relative to NUPACK 3.0, the following change was introduced to the

distributions executable: the -ordered option is on by default.

Use the -v3.0 option to revert to NUPACK 3.0 behavior.

There are 64 populations in Lambda.

Free energy of the box: -1.667768e+01 kT, or -1.629827e-23 kcal

Elapsed time: 0 seconds.

#---maxstates 就是設(shè)置一個(gè)空間來存放計(jì)算數(shù)據(jù)

#---writestates 編寫一個(gè)（通常很大的）輸出文件丰榴，描述系統(tǒng)所有填充狀態(tài)的屬性

#----sort 就是結(jié)果排序的方法

輸出文件

prefix.dist文件內(nèi)容

% NUPACK 3.2.2

% This is /Users/zhangjian/Desktop/prefix.dist, an output file generated for a

% calculation of equilibrium complex count distributions.

% Time calculation was begun: Wed Nov 25 16:24:44 2020

% Inital monomer counts:

%? 1: 1

%? 2: 2

%? 3: 3

% Box volume (liters): 1.400000e-18

3 1 0 0 1 -2.803544e+01 1.023065e+00 1.685686e-06 9.769415e-01 2.304693e-02 9.860647e-06

35 1 1 2 2 -1.622122e+02 9.769412e-01 2.305885e-02 9.769412e-01 0.000000e+00 0.000000e+00

27 1 1 2 1 -1.219707e+02 2.240748e-02 9.775925e-01 2.240748e-02 0.000000e+00 0.000000e+00

2 1 0 1 0 -2.772295e+01 6.514024e-04 9.993487e-01 6.512880e-04 5.719640e-08 0.000000e+00

14 1 1 1 1 -8.176402e+01 6.411420e-04 9.993589e-01 6.411420e-04 0.000000e+00 0.000000e+00

5 1 1 1 0 -4.152258e+01 9.804429e-06 9.999902e-01 9.804429e-06 0.000000e+00 0.000000e+00

9 1 0 0 2 -6.045087e+01 1.687847e-06 9.999983e-01 1.687847e-06 0.000000e+00 0.000000e+00

28 1 1 1 2 -1.153619e+02 3.497095e-07 9.999997e-01 3.497095e-07 0.000000e+00 0.000000e+00

1 1 1 0 0 -7.875853e-01 5.716051e-08 9.999999e-01 5.716051e-08 0.000000e+00 0.000000e+00

35 2 1 2 2 -1.514039e+02 1.032109e-08 1.000000e+00 1.032109e-08 0.000000e+00 0.000000e+00

8 1 0 1 1 -5.911905e+01 8.490297e-09 1.000000e+00 8.490297e-09 1.435566e-17 0.000000e+00

13 1 1 2 0 -7.443309e+01 1.414184e-09 1.000000e+00 1.414184e-09 0.000000e+00 0.000000e+00

28 2 1 1 2 -1.112604e+02 3.287730e-10 1.000000e+00 3.287730e-10 0.000000e+00 0.000000e+00

27 2 1 2 1 -1.105970e+02 9.056463e-11 1.000000e+00 9.056463e-11 0.000000e+00 0.000000e+00

6 1 1 0 1 -3.427792e+01 3.895163e-11 1.000000e+00 3.895163e-11 0.000000e+00 0.000000e+00

14 2 1 1 1 -7.101903e+01 7.542139e-12 1.000000e+00 7.542139e-12 0.000000e+00 0.000000e+00

7 1 0 2 0 -5.889183e+01 8.555047e-13 1.000000e+00 8.555047e-13 0.000000e+00 0.000000e+00

18 1 0 1 2 -9.192658e+01 6.180641e-13 1.000000e+00 6.180641e-13 0.000000e+00 0.000000e+00

19 1 0 0 3 -9.225634e+01 2.806648e-14 1.000000e+00 2.806648e-14 0.000000e+00 0.000000e+00

15 1 1 0 2 -6.762355e+01 1.383906e-14 1.000000e+00 1.383906e-14 0.000000e+00 0.000000e+00

27 3 1 2 1 -1.039379e+02 1.103362e-15 1.000000e+00 1.103362e-15 0.000000e+00 0.000000e+00

prefix.states文件內(nèi)容

% NUPACK 3.2.2

% This is /Users/zhangjian/Desktop/prefix.states, an output file generated for a

% calculation of equilibrium complex count distributions.

% The contents of this file is the Lambda, the set of

% population vectors consistent with conservation of mass.

% Time calculation was begun: Wed Nov 25 16:24:44 2020

5.714489e-08 1 1 1 2 1 2 3 1 3

1.032109e-08 3 1 1 35 2 1

9.769412e-01 3 1 1 35 1 1

5.112064e-21 1 1 1 2 1 1 33 1 1

1.059172e-21 1 1 1 3 1 1 32 2 1

7.420598e-21 1 1 1 3 1 1 32 1 1

2.082922e-18 2 1 2 29 1 1

3.287708e-10 2 1 1 3 1 1 28 2 1

3.497072e-07 2 1 1 3 1 1 28 1 1

1.065891e-15 2 1 1 3 1 1 28 3 1

1.103281e-15 3 1 2 27 3 1

9.055800e-11 3 1 2 27 2 1

2.240584e-02 3 1 2 27 1 1

1.626522e-16 1 1 1 2 1 2 19 1 1

3.158972e-16 1 1 1 2 1 1 3 1 1 18 1 1

2.008982e-17 1 1 1 3 1 2 17 1 1

1.383867e-14 2 1 2 3 1 1 15 1 1

1.621705e-24 15 1 1 17 1 1

7.541490e-12 2 1 1 3 1 2 14 2 1

6.948231e-21 14 2 1 18 1 1

6.410869e-04 2 1 1 3 1 2 14 1 1

5.906551e-13 14 1 1 18 1 1

1.413874e-09 3 1 3 13 1 1

4.024326e-18 13 1 1 19 1 1

1.253896e-11 1 1 1 2 1 2 3 1 1 9 1 1

8.069547e-20 9 1 1 27 3 1

6.623534e-15 9 1 1 27 2 1

1.638793e-06 9 1 1 27 1 1

1.469396e-21 1 1 1 9 1 1 17 1 1

5.515947e-16 2 1 1 9 1 1 14 2 1

4.688995e-08 2 1 1 9 1 1 14 1 1

3.102378e-13 3 1 1 9 1 1 13 1 1

2.218333e-12 1 1 1 2 1 1 3 1 2 8 1 1

2.127116e-15 8 1 1 28 2 1

2.262573e-12 8 1 1 28 1 1

6.896216e-21 8 1 1 28 3 1

2.043825e-21 1 1 1 8 1 1 18 1 1

1.790698e-19 2 1 1 8 1 1 15 1 1

9.758546e-17 3 1 1 8 1 1 14 2 1

8.295543e-09 3 1 1 8 1 1 14 1 1

1.622518e-16 1 1 1 2 1 1 8 1 1 9 1 1

1.435240e-17 1 1 1 3 1 1 8 1 2

8.547344e-13 1 1 1 3 1 3 7 1 1

3.115492e-23 7 1 1 29 1 1

2.432841e-21 1 1 1 7 1 1 19 1 1

2.069894e-19 3 1 1 7 1 1 15 1 1

1.875493e-16 1 1 1 3 1 1 7 1 1 9 1 1

3.894719e-11 2 1 2 3 1 2 6 1 1

2.406269e-25 6 1 1 32 2 1

1.685840e-24 6 1 1 32 1 1

7.176674e-20 2 1 1 6 1 1 18 1 1

9.128166e-21 3 1 1 6 1 1 17 1 1

2.848650e-15 2 1 2 6 1 1 9 1 1

1.007939e-15 2 1 1 3 1 1 6 1 1 8 1 1

3.260634e-21 6 1 1 8 1 2

5.825456e-16 3 1 2 6 1 1 7 1 1

4.260816e-20 6 1 1 7 1 1 9 1 1

9.802088e-06 2 1 1 3 1 3 5 1 1

4.384373e-19 5 1 1 33 1 1

2.789980e-14 2 1 1 5 1 1 19 1 1

2.709299e-14 3 1 1 5 1 1 18 1 1

2.150813e-09 2 1 1 3 1 1 5 1 1 9 1 1

1.902557e-10 3 1 2 5 1 1 8 1 1

1.391556e-14 5 1 1 8 1 1 9 1 1

最后

網(wǎng)站上還像有一個(gè)demo 可以試找試一下看看

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2020-11-14

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