fourfinger

Scaffold Selector Results
10 March 2024 23:22:43

Results

Top Scoring Origamis (on Pareto Front)

SAW Top 5

SAW Rank Origami Id Scaffold Name Rotation Offset G Quad Staples Metric 1 Metric 2 Metric 3 Metric 4 Origami Contact Map Origami Sequences
1 3684 p8064_novopro_432 703 1 285.75
↓-20.4%		 71.36
↓-57.1%		 5.99
↓-35.9%		 0.00
↓-100.0%		 CSV FASTA
2 4888 p8064_novopro_729 703 0 236.39
↓-34.1%		 48.60
↓-70.8%		 7.25
↓-22.4%		 0.00
↓-100.0%		 CSV FASTA
3 1314 lambda_NEB_28727 703 2 243.79
↓-32.1%		 49.74
↓-70.1%		 6.78
↓-27.5%		 0.54
↓-68.8%		 CSV FASTA
4 182 p8064_novopro_731 703 0 175.31
↓-51.2%		 48.60
↓-70.8%		 7.65
↓-18.2%		 0.19
↓-88.7%		 CSV FASTA
5 128 lambda_NEB_28706 703 1 227.46
↓-36.6%		 39.07
↓-76.5%		 7.36
↓-21.3%		 0.82
↓-52.5%		 CSV FASTA

KNEE Top 5

KNEE Rank Origami Id Scaffold Name Rotation Offset G Quad Staples Metric 1 Metric 2 Metric 3 Metric 4 Origami Contact Map Origami Sequences
1 3684 p8064_novopro_432 703 1 285.75
↓-20.4%		 71.36
↓-57.1%		 5.99
↓-35.9%		 0.00
↓-100.0%		 CSV FASTA
2 1314 lambda_NEB_28727 703 2 243.79
↓-32.1%		 49.74
↓-70.1%		 6.78
↓-27.5%		 0.54
↓-68.8%		 CSV FASTA
3 4888 p8064_novopro_729 703 0 236.39
↓-34.1%		 48.60
↓-70.8%		 7.25
↓-22.4%		 0.00
↓-100.0%		 CSV FASTA
4 1431 lambda_NEB_28838 703 1 237.72
↓-33.8%		 64.84
↓-61.0%		 6.67
↓-28.7%		 0.92
↓-46.7%		 CSV FASTA
5 3450 p8064_novopro_543 703 0 264.21
↓-26.4%		 81.05
↓-51.3%		 6.82
↓-27.0%		 0.00
↓-100.0%		 CSV FASTA

TOPSIS Top 5

TOPSIS Rank Origami Id Scaffold Name Rotation Offset G Quad Staples Metric 1 Metric 2 Metric 3 Metric 4 Origami Contact Map Origami Sequences
1 3684 p8064_novopro_432 703 1 285.75
↓-20.4%		 71.36
↓-57.1%		 5.99
↓-35.9%		 0.00
↓-100.0%		 CSV FASTA
2 1314 lambda_NEB_28727 703 2 243.79
↓-32.1%		 49.74
↓-70.1%		 6.78
↓-27.5%		 0.54
↓-68.8%		 CSV FASTA
3 4888 p8064_novopro_729 703 0 236.39
↓-34.1%		 48.60
↓-70.8%		 7.25
↓-22.4%		 0.00
↓-100.0%		 CSV FASTA
4 1431 lambda_NEB_28838 703 1 237.72
↓-33.8%		 64.84
↓-61.0%		 6.67
↓-28.7%		 0.92
↓-46.7%		 CSV FASTA
5 3450 p8064_novopro_543 703 0 264.21
↓-26.4%		 81.05
↓-51.3%		 6.82
↓-27.0%		 0.00
↓-100.0%		 CSV FASTA

Settings Used

Origami

Origami Scaffold-Staples Material Energy Model Scaffold Num Staples
fourfinger DNA-DNA DNA 704 nt, LINEAR 24

Selection Mode & Metrics Used

MODE 2 - Score a sample pool of unique scaffold sequences        Run on local machine        NUPACK v4.0.1.8

  Used Description Unit Weight
Metric 1 ✔ Staple-Scaffold: Total energy of off-target staple binding sites kcal/mol Absolute Value 0.25
Metric 2 ✔ Intra Scaffold: Total energy of scaffold-scaffold binding sites kcal/mol Absolute Value 0.25
Metric 3 ✔ Staple-Staple: Worst binding energy between two staples kcal/mol Absolute Value 0.25
Metric 4 ✔ Intra Staple: Worst secondary structure energy of a single staple kcal/mol Absolute Value 0.25

Scaffold Pool

5000 sequences sampled from biological_vectors.csv each of length 704 nt [python3 generate.py 5000 biological_vectors.csv 704 fourfinger_scaffolds.csv]   [ CSV ]

Final Origami Pool Selected From

Scaffold sequences in the scaffold pool are not rotated. Origami rotation number forced to R = 1.

Origami Rotation Number, R x Scaffold Pool Size = Total Origami Pool Size Origamis Scored % Total Pool Coverage
1 5000 5000 5000 100

Other Information

Objective Space (4 Dimensional)

Origamis Scored Number on Pareto Front % Origamis on Pareto Front Total Number Dominated ..of which on Reverse Front % Origamis on Reverse Front Objective Space Data
5000 92 1.84 4908 57 1.14 CSV

Metric Distributions in Objective Space

Distributions Mean Standard Dev. Min Max Pareto Centroid Reverse Pareto Centroid Histogram Raw Data
Metric 1 358.94 136.83 100.90 1553.85 229.98 751.02 CSV
Metric 2 166.46 48.33 39.07 347.93 115.55 232.53 CSV
Metric 3 9.35 1.65 5.64 15.00 7.46 12.31 CSV
Metric 4 1.73 1.22 0 8.55 0.86 3.76 CSV
Relative Changes Max → Min Value Pop Centroid → Pareto Centroid Pop Centroid → Reverse Pareto Centroid Reverse Pareto Centroid → Pareto Centroid
Metric 1 ↓-93.5% ↓-35.9% ↑+109.2% ↓-69.4%
Metric 2 ↓-88.8% ↓-30.6% ↑+39.7% ↓-50.3%
Metric 3 ↓-62.4% ↓-20.2% ↑+31.6% ↓-39.4%
Metric 4 ↓-100.0% ↓-50.4% ↑+118.1% ↓-77.3%

Origamis Minimising and Maximising Individual Metrics

Origami Description Origami Id Scaffold Name Rotation Offset G Quad Staples Metric 1 Metric 2 Metric 3 Metric 4 Origami Contact Map Origami Sequences
M1 Min Origami 101 pUC19_NEB_1860 703 1 100.90
↓-71.9%		 116.45
↓-30.0%		 7.99
↓-14.6%		 0.87
↓-49.4%		 CSV FASTA
M1 Max Origami 4312 p8064_novopro_1774 703 2 1553.85
↑+332.9%		 69.62
↓-58.2%		 7.88
↓-15.7%		 1.02
↓-40.9%		 CSV FASTA
M2 Min Origami 128 lambda_NEB_28706 703 1 227.46
↓-36.6%		 39.07
↓-76.5%		 7.36
↓-21.3%		 0.82
↓-52.5%		 CSV FASTA
M2 Max Origami 3611 lambda_NEB_19859 703 0 846.50
↑+135.8%		 347.93
↑+109.0%		 10.93
↑+16.9%		 3.15
↑+82.4%		 CSV FASTA
M3 Min Origami 4341 p8064_novopro_3591 703 0 600.79
↑+67.4%		 236.95
↑+42.3%		 5.64
↓-39.6%		 0.62
↓-64.3%		 CSV FASTA
M3 Max Origami 4916 p8064_novopro_5452 703 2 273.04
↓-23.9%		 218.83
↑+31.5%		 15.00
↑+60.4%		 3.71
↑+115.3%		 CSV FASTA
M4 Min Origami 29 lambda_NEB_26347 703 0 306.01
↓-14.7%		 176.23
↑+5.9%		 7.62
↓-18.5%		 0.00
↓-100.0%		 CSV FASTA
M4 Max Origami 4783 lambda_NEB_5335 703 2 543.78
↑+51.5%		 246.55
↑+48.1%		 12.10
↑+29.5%		 8.55
↑+395.4%		 CSV FASTA

Worst Scoring Origamis (on Reverse Pareto Front)

SAW Top 5

SAW Rank Origami Id Scaffold Name Rotation Offset Metric 1 Metric 2 Metric 3 Metric 4 Origami Contact Map Origami Sequences
1 4648 lambda_NEB_19987 703 1161.69
↑+223.6%		 298.69
↑+79.4%		 14.36
↑+53.6%		 4.94
↑+186.1%		 CSV FASTA
2 2173 lambda_NEB_19979 703 1131.01
↑+215.1%		 298.76
↑+79.5%		 14.36
↑+53.6%		 4.17
↑+141.7%		 CSV FASTA
3 2450 lambda_NEB_19951 703 1042.25
↑+190.4%		 307.84
↑+84.9%		 12.91
↑+38.1%		 5.14
↑+197.6%		 CSV FASTA
4 1147 lambda_NEB_19875 703 855.14
↑+138.2%		 341.30
↑+105.0%		 14.36
↑+53.6%		 2.81
↑+62.8%		 CSV FASTA
5 4772 lambda_NEB_19907 703 906.71
↑+152.6%		 336.23
↑+102.0%		 13.56
↑+45.0%		 3.18
↑+84.4%		 CSV FASTA

KNEE Top 5

KNEE Rank Origami Id Scaffold Name Rotation Offset Metric 1 Metric 2 Metric 3 Metric 4 Origami Contact Map Origami Sequences
1 4648 lambda_NEB_19987 703 1161.69
↑+223.6%		 298.69
↑+79.4%		 14.36
↑+53.6%		 4.94
↑+186.1%		 CSV FASTA
2 2450 lambda_NEB_19951 703 1042.25
↑+190.4%		 307.84
↑+84.9%		 12.91
↑+38.1%		 5.14
↑+197.6%		 CSV FASTA
3 2173 lambda_NEB_19979 703 1131.01
↑+215.1%		 298.76
↑+79.5%		 14.36
↑+53.6%		 4.17
↑+141.7%		 CSV FASTA
4 2923 lambda_NEB_20037 703 1294.03
↑+260.5%		 300.72
↑+80.7%		 11.23
↑+20.1%		 3.56
↑+106.0%		 CSV FASTA
5 1824 lambda_NEB_19974 703 1086.57
↑+202.7%		 300.21
↑+80.4%		 11.15
↑+19.2%		 4.17
↑+141.7%		 CSV FASTA

TOPSIS Top 5

TOPSIS Rank Origami Id Scaffold Name Rotation Offset Metric 1 Metric 2 Metric 3 Metric 4 Origami Contact Map Origami Sequences
1 4648 lambda_NEB_19987 703 1161.69
↑+223.6%		 298.69
↑+79.4%		 14.36
↑+53.6%		 4.94
↑+186.1%		 CSV FASTA
2 2173 lambda_NEB_19979 703 1131.01
↑+215.1%		 298.76
↑+79.5%		 14.36
↑+53.6%		 4.17
↑+141.7%		 CSV FASTA
3 2450 lambda_NEB_19951 703 1042.25
↑+190.4%		 307.84
↑+84.9%		 12.91
↑+38.1%		 5.14
↑+197.6%		 CSV FASTA
4 2923 lambda_NEB_20037 703 1294.03
↑+260.5%		 300.72
↑+80.7%		 11.23
↑+20.1%		 3.56
↑+106.0%		 CSV FASTA
5 4772 lambda_NEB_19907 703 906.71
↑+152.6%		 336.23
↑+102.0%		 13.56
↑+45.0%		 3.18
↑+84.4%		 CSV FASTA

Metric Score Pairwise Correlations

Pearson's r Metric 1 Metric 2 Metric 3 Metric 4
Metric 1 1.00 0.23 0.06 0.07
Metric 2 0.23 1 0.13 0.11
Metric 3 0.06 0.13 1 0.33
Metric 4 0.07 0.11 0.33 1
Spearman's r Metric 1 Metric 2 Metric 3 Metric 4
Metric 1 1 0.26 0.08 0.07
Metric 2 0.26 1 0.11 0.07
Metric 3 0.08 0.11 1 0.36
Metric 4 0.07 0.07 0.36 1

Metric Individual Execution Times

  Mean Execution Time (s) Min Execution Time (s) Max Execution Time (s)
Metric 1 0.2359 0.2262 0.3395
Metric 2 0.1113 0.1055 0.1377
Metric 3 0.3042 0.2499 0.3804
Metric 4 0.0105 0.0086 0.0212

Whole Job Estimated Run Time on Single CPU

00:55:09