tri

Scaffold Selector Results
24 March 2024 19:28:19

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 2422 >scaffold2422__lambda_NEB_28733__5to3prime 2409 3 2661.96
↓-26.8%		 1367.57
↓-28.5%		 8.71
↓-21.8%		 1.28
↓-57.1%		 CSV FASTA
2 2499 >scaffold2499__lambda_NEB_28731__5to3prime 2409 3 2611.72
↓-28.2%		 1367.57
↓-28.5%		 9.37
↓-15.9%		 1.28
↓-57.1%		 CSV FASTA
3 340 >scaffold340__lambda_NEB_28672__5to3prime 2409 5 2756.80
↓-24.2%		 1416.63
↓-26.0%		 8.14
↓-26.9%		 1.88
↓-36.9%		 CSV FASTA
4 1545 >scaffold1545__lambda_NEB_28729__5to3prime 2409 3 2635.43
↓-27.5%		 1360.02
↓-28.9%		 9.39
↓-15.7%		 1.83
↓-38.7%		 CSV FASTA
5 3733 >scaffold3733__lambda_NEB_29152__5to3prime 2409 3 2626.73
↓-27.8%		 1599.12
↓-16.4%		 8.35
↓-25.0%		 1.28
↓-57.1%		 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 2422 >scaffold2422__lambda_NEB_28733__5to3prime 2409 3 2661.96
↓-26.8%		 1367.57
↓-28.5%		 8.71
↓-21.8%		 1.28
↓-57.1%		 CSV FASTA
2 2499 >scaffold2499__lambda_NEB_28731__5to3prime 2409 3 2611.72
↓-28.2%		 1367.57
↓-28.5%		 9.37
↓-15.9%		 1.28
↓-57.1%		 CSV FASTA
3 340 >scaffold340__lambda_NEB_28672__5to3prime 2409 5 2756.80
↓-24.2%		 1416.63
↓-26.0%		 8.14
↓-26.9%		 1.88
↓-36.9%		 CSV FASTA
4 1545 >scaffold1545__lambda_NEB_28729__5to3prime 2409 3 2635.43
↓-27.5%		 1360.02
↓-28.9%		 9.39
↓-15.7%		 1.83
↓-38.7%		 CSV FASTA
5 3733 >scaffold3733__lambda_NEB_29152__5to3prime 2409 3 2626.73
↓-27.8%		 1599.12
↓-16.4%		 8.35
↓-25.0%		 1.28
↓-57.1%		 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 2422 >scaffold2422__lambda_NEB_28733__5to3prime 2409 3 2661.96
↓-26.8%		 1367.57
↓-28.5%		 8.71
↓-21.8%		 1.28
↓-57.1%		 CSV FASTA
2 2499 >scaffold2499__lambda_NEB_28731__5to3prime 2409 3 2611.72
↓-28.2%		 1367.57
↓-28.5%		 9.37
↓-15.9%		 1.28
↓-57.1%		 CSV FASTA
3 340 >scaffold340__lambda_NEB_28672__5to3prime 2409 5 2756.80
↓-24.2%		 1416.63
↓-26.0%		 8.14
↓-26.9%		 1.88
↓-36.9%		 CSV FASTA
4 1545 >scaffold1545__lambda_NEB_28729__5to3prime 2409 3 2635.43
↓-27.5%		 1360.02
↓-28.9%		 9.39
↓-15.7%		 1.83
↓-38.7%		 CSV FASTA
5 3733 >scaffold3733__lambda_NEB_29152__5to3prime 2409 3 2626.73
↓-27.8%		 1599.12
↓-16.4%		 8.35
↓-25.0%		 1.28
↓-57.1%		 CSV FASTA

Settings Used

Origami

Origami Scaffold-Staples Material Energy Model Scaffold Num Staples
tri DNA-DNA DNA 2410 nt, LINEAR 66

Selection Mode & Metrics Used

MODE 2 - Score a sample pool of unique scaffold sequences        Run on cluster        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 Biological Vector Segments   [ 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 207 4.14 4793 135 2.70 CSV

Metric Distributions in Objective Space

Distributions Mean Standard Dev. Min Max Pareto Centroid Reverse Pareto Centroid Histogram Raw Data
Metric 1 3636.11 704.83 2139.97 5735.41 3270.20 4607.48 CSV
Metric 2 1913.25 318.38 1226.54 2680.68 1665.20 2362.02 CSV
Metric 3 11.14 1.48 7.33 17.78 9.55 13.05 CSV
Metric 4 2.99 1.30 0 10.00 1.55 4.45 CSV
Relative Changes Max → Min Value Pop Centroid → Pareto Centroid Pop Centroid → Reverse Pareto Centroid Reverse Pareto Centroid → Pareto Centroid
Metric 1 ↓-62.7% ↓-10.1% ↑+26.7% ↓-29.0%
Metric 2 ↓-54.2% ↓-13.0% ↑+23.5% ↓-29.5%
Metric 3 ↓-58.8% ↓-14.2% ↑+17.2% ↓-26.8%
Metric 4 ↓-100.0% ↓-48.1% ↑+48.8% ↓-65.1%

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 2941 >scaffold2941__pUC19_NEB_902__5to3prime 2409 5 2139.97
↓-41.1%		 1561.57
↓-18.4%		 11.80
↑+6.0%		 2.55
↓-14.5%		 CSV FASTA
M1 Max Origami 648 >scaffold648__lambda_NEB_10376__5to3prime 2409 1 5735.41
↑+57.7%		 2183.59
↑+14.1%		 11.28
↑+1.3%		 5.14
↑+72.1%		 CSV FASTA
M2 Min Origami 1721 >scaffold1721__p8064_novopro_520__5to3prime 2409 3 4429.16
↑+21.8%		 1226.54
↓-35.9%		 9.23
↓-17.2%		 1.29
↓-56.7%		 CSV FASTA
M2 Max Origami 2972 >scaffold2972__lambda_NEB_15423__5to3prime 2409 1 4251.55
↑+16.9%		 2680.68
↑+40.1%		 11.44
↑+2.7%		 4.68
↑+56.8%		 CSV FASTA
M3 Min Origami 4744 >scaffold4744__lambda_NEB_23851__5to3prime 2409 0 3484.99
↓-4.2%		 1975.12
↑+3.2%		 7.33
↓-34.2%		 2.12
↓-28.9%		 CSV FASTA
M3 Max Origami 3296 >scaffold3296__lambda_NEB_11543__5to3prime 2409 2 4921.32
↑+35.3%		 2196.37
↑+14.8%		 17.78
↑+59.7%		 2.12
↓-28.9%		 CSV FASTA
M4 Min Origami 150 >scaffold150__lambda_NEB_25641__5to3prime 2409 2 3252.51
↓-10.5%		 2174.17
↑+13.6%		 10.70
↓-3.9%		 0.00
↓-100.0%		 CSV FASTA
M4 Max Origami 4096 >scaffold4096__lambda_NEB_29405__5to3prime 2409 4 2902.23
↓-20.2%		 1650.00
↓-13.8%		 9.60
↓-13.8%		 10.00
↑+234.7%		 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 1158 >scaffold1158__lambda_NEB_10408__5to3prime 2409 5703.40
↑+56.9%		 2173.72
↑+13.6%		 12.55
↑+12.7%		 7.01
↑+134.8%		 CSV FASTA
2 4801 >scaffold4801__lambda_NEB_10176__5to3prime 2409 5453.45
↑+50.0%		 2262.43
↑+18.3%		 13.67
↑+22.8%		 5.83
↑+95.0%		 CSV FASTA
3 2356 >scaffold2356__lambda_NEB_10765__5to3prime 2409 5428.66
↑+49.3%		 2058.49
↑+7.6%		 13.17
↑+18.3%		 7.77
↑+160.2%		 CSV FASTA
4 1162 >scaffold1162__lambda_NEB_15272__5to3prime 2409 4284.03
↑+17.8%		 2589.52
↑+35.3%		 13.46
↑+20.9%		 6.91
↑+131.2%		 CSV FASTA
5 46 >scaffold46__lambda_NEB_3594__5to3prime 2409 4212.30
↑+15.8%		 2578.80
↑+34.8%		 12.42
↑+11.5%		 8.09
↑+170.9%		 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 4801 >scaffold4801__lambda_NEB_10176__5to3prime 2409 5453.45
↑+50.0%		 2262.43
↑+18.3%		 13.67
↑+22.8%		 5.83
↑+95.0%		 CSV FASTA
2 1432 >scaffold1432__lambda_NEB_6980__5to3prime 2409 4915.29
↑+35.2%		 2141.35
↑+11.9%		 14.36
↑+28.9%		 6.39
↑+114.0%		 CSV FASTA
3 1162 >scaffold1162__lambda_NEB_15272__5to3prime 2409 4284.03
↑+17.8%		 2589.52
↑+35.3%		 13.46
↑+20.9%		 6.91
↑+131.2%		 CSV FASTA
4 2356 >scaffold2356__lambda_NEB_10765__5to3prime 2409 5428.66
↑+49.3%		 2058.49
↑+7.6%		 13.17
↑+18.3%		 7.77
↑+160.2%		 CSV FASTA
5 3854 >scaffold3854__lambda_NEB_10761__5to3prime 2409 5100.16
↑+40.3%		 2050.94
↑+7.2%		 13.33
↑+19.7%		 7.88
↑+163.6%		 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 4801 >scaffold4801__lambda_NEB_10176__5to3prime 2409 5453.45
↑+50.0%		 2262.43
↑+18.3%		 13.67
↑+22.8%		 5.83
↑+95.0%		 CSV FASTA
2 2356 >scaffold2356__lambda_NEB_10765__5to3prime 2409 5428.66
↑+49.3%		 2058.49
↑+7.6%		 13.17
↑+18.3%		 7.77
↑+160.2%		 CSV FASTA
3 1162 >scaffold1162__lambda_NEB_15272__5to3prime 2409 4284.03
↑+17.8%		 2589.52
↑+35.3%		 13.46
↑+20.9%		 6.91
↑+131.2%		 CSV FASTA
4 1158 >scaffold1158__lambda_NEB_10408__5to3prime 2409 5703.40
↑+56.9%		 2173.72
↑+13.6%		 12.55
↑+12.7%		 7.01
↑+134.8%		 CSV FASTA
5 3854 >scaffold3854__lambda_NEB_10761__5to3prime 2409 5100.16
↑+40.3%		 2050.94
↑+7.2%		 13.33
↑+19.7%		 7.88
↑+163.6%		 CSV FASTA

Metric Score Pairwise Correlations

Pearson's r Metric 1 Metric 2 Metric 3 Metric 4
Metric 1 1.00 0.57 0.18 0.18
Metric 2 0.57 1 0.31 0.30
Metric 3 0.18 0.31 1 0.32
Metric 4 0.18 0.30 0.32 1.00
Spearman's r Metric 1 Metric 2 Metric 3 Metric 4
Metric 1 1 0.60 0.22 0.20
Metric 2 0.60 1 0.33 0.32
Metric 3 0.22 0.33 1 0.35
Metric 4 0.20 0.32 0.35 1

Metric Individual Execution Times

  Mean Execution Time (s) Min Execution Time (s) Max Execution Time (s)
Metric 1 10.6479 7.5556 25.8101
Metric 2 5.7463 4.0022 14.6913
Metric 3 20.2628 13.4066 93.3409
Metric 4 0.3040 0.2066 1.1190

Whole Job Estimated Run Time on Single CPU

2 Days + 03:20:04