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Scaffold Selector Results
22 March 2024 23:04:22

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	3266	>scaffold3266__lambda_NEB_28639__5to3prime	2483	2	2975.13 ↓-27.3%	1514.40 ↓-25.0%	8.52 ↓-24.2%	1.57 ↓-49.0%	CSV	FASTA
2	1154	>scaffold1154__lambda_NEB_28777__5to3prime	2483	4	3116.11 ↓-23.9%	1494.27 ↓-26.0%	8.52 ↓-24.2%	1.57 ↓-49.0%	CSV	FASTA
3	2876	>scaffold2876__lambda_NEB_28629__5to3prime	2483	3	2996.77 ↓-26.8%	1514.40 ↓-25.0%	9.14 ↓-18.7%	1.49 ↓-51.8%	CSV	FASTA
4	1027	>scaffold1027__lambda_NEB_40069__5to3prime	2483	0	3250.33 ↓-20.6%	1520.54 ↓-24.7%	8.70 ↓-22.7%	1.46 ↓-52.8%	CSV	FASTA
5	3344	>scaffold3344__lambda_NEB_28844__5to3prime	2483	3	2899.58 ↓-29.2%	1493.53 ↓-26.0%	8.29 ↓-26.3%	3.03 ↓-1.7%	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	3266	>scaffold3266__lambda_NEB_28639__5to3prime	2483	2	2975.13 ↓-27.3%	1514.40 ↓-25.0%	8.52 ↓-24.2%	1.57 ↓-49.0%	CSV	FASTA
2	1154	>scaffold1154__lambda_NEB_28777__5to3prime	2483	4	3116.11 ↓-23.9%	1494.27 ↓-26.0%	8.52 ↓-24.2%	1.57 ↓-49.0%	CSV	FASTA
3	2876	>scaffold2876__lambda_NEB_28629__5to3prime	2483	3	2996.77 ↓-26.8%	1514.40 ↓-25.0%	9.14 ↓-18.7%	1.49 ↓-51.8%	CSV	FASTA
4	1027	>scaffold1027__lambda_NEB_40069__5to3prime	2483	0	3250.33 ↓-20.6%	1520.54 ↓-24.7%	8.70 ↓-22.7%	1.46 ↓-52.8%	CSV	FASTA
5	1069	>scaffold1069__lambda_NEB_29130__5to3prime	2483	4	3046.30 ↓-25.6%	1644.42 ↓-18.5%	9.12 ↓-18.9%	1.26 ↓-59.2%	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	3266	>scaffold3266__lambda_NEB_28639__5to3prime	2483	2	2975.13 ↓-27.3%	1514.40 ↓-25.0%	8.52 ↓-24.2%	1.57 ↓-49.0%	CSV	FASTA
2	1154	>scaffold1154__lambda_NEB_28777__5to3prime	2483	4	3116.11 ↓-23.9%	1494.27 ↓-26.0%	8.52 ↓-24.2%	1.57 ↓-49.0%	CSV	FASTA
3	2876	>scaffold2876__lambda_NEB_28629__5to3prime	2483	3	2996.77 ↓-26.8%	1514.40 ↓-25.0%	9.14 ↓-18.7%	1.49 ↓-51.8%	CSV	FASTA
4	1027	>scaffold1027__lambda_NEB_40069__5to3prime	2483	0	3250.33 ↓-20.6%	1520.54 ↓-24.7%	8.70 ↓-22.7%	1.46 ↓-52.8%	CSV	FASTA
5	1069	>scaffold1069__lambda_NEB_29130__5to3prime	2483	4	3046.30 ↓-25.6%	1644.42 ↓-18.5%	9.12 ↓-18.9%	1.26 ↓-59.2%	CSV	FASTA

Settings Used

Origami

Origami	Scaffold-Staples Material	Energy Model	Scaffold	Num Staples
rect	DNA-DNA	DNA	2484 nt, LINEAR	70

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

5K 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	200	4	4800	114	2.28	CSV

Metric Distributions in Objective Space

Distributions	Mean	Standard Dev.	Min	Max	Pareto Centroid	Reverse Pareto Centroid	Histogram Raw Data
Metric 1	4092.82	806.61	2431.14	6622.94	3762.23	5315.03	CSV
Metric 2	2018.84	335.26	1315.23	2858.76	1754.65	2532.93	CSV
Metric 3	11.25	1.47	7.43	18.13	9.70	12.56	CSV
Metric 4	3.09	1.27	0	9.79	1.67	4.61	CSV

Relative Changes	Max → Min Value	Pop Centroid → Pareto Centroid	Pop Centroid → Reverse Pareto Centroid	Reverse Pareto Centroid → Pareto Centroid
Metric 1	↓-63.3%	↓-8.1%	↑+29.9%	↓-29.2%
Metric 2	↓-54.0%	↓-13.1%	↑+25.5%	↓-30.7%
Metric 3	↓-59.0%	↓-13.8%	↑+11.7%	↓-22.8%
Metric 4	↓-100.0%	↓-45.7%	↑+49.5%	↓-63.7%

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	183	>scaffold183__pUC19_NEB_683__5to3prime	2483	5	2431.14 ↓-40.6%	1670.25 ↓-17.3%	10.82 ↓-3.8%	2.40 ↓-22.4%	CSV	FASTA
M1 Max Origami	3339	>scaffold3339__lambda_NEB_10604__5to3prime	2483	1	6622.94 ↑+61.8%	2296.96 ↑+13.8%	11.80 ↑+4.9%	2.46 ↓-20.2%	CSV	FASTA
M2 Min Origami	165	>scaffold165__p8064_novopro_624__5to3prime	2483	1	5120.93 ↑+25.1%	1315.23 ↓-34.9%	8.87 ↓-21.1%	1.99 ↓-35.6%	CSV	FASTA
M2 Max Origami	4118	>scaffold4118__lambda_NEB_3730__5to3prime	2483	3	4978.92 ↑+21.7%	2858.76 ↑+41.6%	12.86 ↑+14.3%	3.70 ↑+19.9%	CSV	FASTA
M3 Min Origami	1620	>scaffold1620__lambda_NEB_23230__5to3prime	2483	0	4624.24 ↑+13.0%	2380.56 ↑+17.9%	7.43 ↓-33.9%	2.64 ↓-14.5%	CSV	FASTA
M3 Max Origami	3711	>scaffold3711__p8064_novopro_4827__5to3prime	2483	5	3612.67 ↓-11.7%	1983.84 ↓-1.7%	18.13 ↑+61.2%	3.32 ↑+7.5%	CSV	FASTA
M4 Min Origami	1888	>scaffold1888__lambda_NEB_22152__5to3prime	2483	1	5000.04 ↑+22.2%	2636.30 ↑+30.6%	10.63 ↓-5.5%	0.00 ↓-100.0%	CSV	FASTA
M4 Max Origami	2463	>scaffold2463__lambda_NEB_4977__5to3prime	2483	6	4278.81 ↑+4.5%	2286.51 ↑+13.3%	12.12 ↑+7.8%	9.79 ↑+217.4%	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	2088	>scaffold2088__lambda_NEB_4204__5to3prime	2483	5148.29 ↑+25.8%	2713.22 ↑+34.4%	17.14 ↑+52.4%	4.73 ↑+53.3%	CSV	FASTA
2	3454	>scaffold3454__lambda_NEB_3235__5to3prime	2483	5190.03 ↑+26.8%	2631.77 ↑+30.4%	13.49 ↑+19.9%	8.17 ↑+164.9%	CSV	FASTA
3	2346	>scaffold2346__lambda_NEB_18723__5to3prime	2483	5093.12 ↑+24.4%	2355.31 ↑+16.7%	16.41 ↑+45.9%	6.86 ↑+122.3%	CSV	FASTA
4	4016	>scaffold4016__lambda_NEB_10137__5to3prime	2483	6384.03 ↑+56.0%	2377.79 ↑+17.8%	13.85 ↑+23.1%	5.83 ↑+88.9%	CSV	FASTA
5	1194	>scaffold1194__lambda_NEB_9875__5to3prime	2483	5605.03 ↑+36.9%	2372.79 ↑+17.5%	15.93 ↑+41.6%	5.28 ↑+71.2%	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	3454	>scaffold3454__lambda_NEB_3235__5to3prime	2483	5190.03 ↑+26.8%	2631.77 ↑+30.4%	13.49 ↑+19.9%	8.17 ↑+164.9%	CSV	FASTA
2	2346	>scaffold2346__lambda_NEB_18723__5to3prime	2483	5093.12 ↑+24.4%	2355.31 ↑+16.7%	16.41 ↑+45.9%	6.86 ↑+122.3%	CSV	FASTA
3	2088	>scaffold2088__lambda_NEB_4204__5to3prime	2483	5148.29 ↑+25.8%	2713.22 ↑+34.4%	17.14 ↑+52.4%	4.73 ↑+53.3%	CSV	FASTA
4	1194	>scaffold1194__lambda_NEB_9875__5to3prime	2483	5605.03 ↑+36.9%	2372.79 ↑+17.5%	15.93 ↑+41.6%	5.28 ↑+71.2%	CSV	FASTA
5	4016	>scaffold4016__lambda_NEB_10137__5to3prime	2483	6384.03 ↑+56.0%	2377.79 ↑+17.8%	13.85 ↑+23.1%	5.83 ↑+88.9%	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	3454	>scaffold3454__lambda_NEB_3235__5to3prime	2483	5190.03 ↑+26.8%	2631.77 ↑+30.4%	13.49 ↑+19.9%	8.17 ↑+164.9%	CSV	FASTA
2	2346	>scaffold2346__lambda_NEB_18723__5to3prime	2483	5093.12 ↑+24.4%	2355.31 ↑+16.7%	16.41 ↑+45.9%	6.86 ↑+122.3%	CSV	FASTA
3	2088	>scaffold2088__lambda_NEB_4204__5to3prime	2483	5148.29 ↑+25.8%	2713.22 ↑+34.4%	17.14 ↑+52.4%	4.73 ↑+53.3%	CSV	FASTA
4	4016	>scaffold4016__lambda_NEB_10137__5to3prime	2483	6384.03 ↑+56.0%	2377.79 ↑+17.8%	13.85 ↑+23.1%	5.83 ↑+88.9%	CSV	FASTA
5	1194	>scaffold1194__lambda_NEB_9875__5to3prime	2483	5605.03 ↑+36.9%	2372.79 ↑+17.5%	15.93 ↑+41.6%	5.28 ↑+71.2%	CSV	FASTA

Metric Score Pairwise Correlations

	Pearson's r	Metric 1	Metric 2	Metric 3	Metric 4
	Metric 1	1.00	0.60	0.19	0.21
	Metric 2	0.60	1.00	0.27	0.26
	Metric 3	0.19	0.27	1	0.33
	Metric 4	0.21	0.26	0.33	1.00

	Spearman's r	Metric 1	Metric 2	Metric 3	Metric 4
	Metric 1	1.00	0.61	0.22	0.21
	Metric 2	0.61	1	0.30	0.28
	Metric 3	0.22	0.30	1	0.35
	Metric 4	0.21	0.28	0.35	1

Metric Individual Execution Times

	Mean Execution Time (s)	Min Execution Time (s)	Max Execution Time (s)
Metric 1	11.6297	9.6638	30.2358
Metric 2	5.8988	4.8615	15.1417
Metric 3	21.3999	15.6816	95.6363
Metric 4	0.2935	0.2267	1.2861

Whole Job Estimated Run Time on Single CPU

2 Days + 06:28:29