fourfinger-circ

Scaffold Selector Results
11 March 2024 09:50:51

Results

Top Scoring Origamis (on Pareto Front)

SAW Top 5

SAW Rank	Origami Id	Scaffold Name	Rotation Offset	G Quad Staples	Metric 1	Metric 3	Metric 4	Origami Contact Map	Origami Sequences
1	653	original scaffold	653	1	152.92 ↓-41.7% ↓-34.4%	8.65 ↓-16.3% ↓-21.5%	1.15 ↓-44.1% ↑+8.5%	CSV	FASTA
2	335	original scaffold	335	2	187.70 ↓-28.5% ↓-19.5%	7.91 ↓-23.4% ↓-28.2%	1.32 ↓-35.6% ↑+24.9%	CSV	FASTA
3	126	original scaffold	126	2	186.44 ↓-28.9% ↓-20.1%	7.99 ↓-22.7% ↓-27.5%	1.29 ↓-36.9% ↑+22.4%	CSV	FASTA
4	47	original scaffold	47	3	196.44 ↓-25.1% ↓-15.8%	9.39 ↓-9.1% ↓-14.8%	0.04 ↓-98.2% ↓-96.5%	CSV	FASTA
5	37	original scaffold	37	3	229.50 ↓-12.5% ↓-1.6%	8.47 ↓-18.0% ↓-23.1%	0.11 ↓-94.6% ↓-89.5%	CSV	FASTA

KNEE Top 5

KNEE Rank	Origami Id	Scaffold Name	Rotation Offset	G Quad Staples	Metric 1	Metric 3	Metric 4	Origami Contact Map	Origami Sequences
1	653	original scaffold	653	1	152.92 ↓-41.7% ↓-34.4%	8.65 ↓-16.3% ↓-21.5%	1.15 ↓-44.1% ↑+8.5%	CSV	FASTA
2	126	original scaffold	126	2	186.44 ↓-28.9% ↓-20.1%	7.99 ↓-22.7% ↓-27.5%	1.29 ↓-36.9% ↑+22.4%	CSV	FASTA
3	335	original scaffold	335	2	187.70 ↓-28.5% ↓-19.5%	7.91 ↓-23.4% ↓-28.2%	1.32 ↓-35.6% ↑+24.9%	CSV	FASTA
4	588	original scaffold	588	3	206.44 ↓-21.3% ↓-11.5%	8.42 ↓-18.5% ↓-23.6%	0.94 ↓-54.3% ↓-11.3%	CSV	FASTA
5	47	original scaffold	47	3	196.44 ↓-25.1% ↓-15.8%	9.39 ↓-9.1% ↓-14.8%	0.04 ↓-98.2% ↓-96.5%	CSV	FASTA

TOPSIS Top 5

TOPSIS Rank	Origami Id	Scaffold Name	Rotation Offset	G Quad Staples	Metric 1	Metric 3	Metric 4	Origami Contact Map	Origami Sequences
1	653	original scaffold	653	1	152.92 ↓-41.7% ↓-34.4%	8.65 ↓-16.3% ↓-21.5%	1.15 ↓-44.1% ↑+8.5%	CSV	FASTA
2	126	original scaffold	126	2	186.44 ↓-28.9% ↓-20.1%	7.99 ↓-22.7% ↓-27.5%	1.29 ↓-36.9% ↑+22.4%	CSV	FASTA
3	335	original scaffold	335	2	187.70 ↓-28.5% ↓-19.5%	7.91 ↓-23.4% ↓-28.2%	1.32 ↓-35.6% ↑+24.9%	CSV	FASTA
4	588	original scaffold	588	3	206.44 ↓-21.3% ↓-11.5%	8.42 ↓-18.5% ↓-23.6%	0.94 ↓-54.3% ↓-11.3%	CSV	FASTA
5	47	original scaffold	47	3	196.44 ↓-25.1% ↓-15.8%	9.39 ↓-9.1% ↓-14.8%	0.04 ↓-98.2% ↓-96.5%	CSV	FASTA

Settings Used

Origami

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

Selection Mode & Metrics Used

MODE 1 - Score all rotations of a fixed scaffold sequence 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	0.33
Metric 2	❌	Intra Scaffold: Total energy of scaffold-scaffold binding sites	kcal/mol Absolute Value	0
Metric 3	✔	Staple-Staple: Worst binding energy between two staples	kcal/mol Absolute Value	0.33
Metric 4	✔	Intra Staple: Worst secondary structure energy of a single staple	kcal/mol Absolute Value	0.33

Scaffold Pool

Original origami scaffold sequence [ CSV ]

Final Origami Pool Selected From

Origami Rotation Number, R	x Scaffold Pool Size	= Total Origami Pool Size	Origamis Scored	% Total Pool Coverage
704	1	704	704	100

Other Information

Objective Space (3 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
704	30	4.26	674	19	2.70	CSV

Open Objective Space plot below in a new window

Metric Distributions in Objective Space

Distributions	Mean	Standard Dev.	Min	Max	Pareto Centroid	Reverse Pareto Centroid	Histogram Raw Data
Metric 1	262.41	37.57	138.92	379.69	225.10	315.76	CSV
Metric 3	10.33	1.51	7.10	14.39	8.60	11.93	CSV
Metric 4	2.05	1.23	0	7.96	1.23	4.11	CSV

Relative Changes	Max → Min Value	Pop Centroid → Pareto Centroid	Pop Centroid → Reverse Pareto Centroid	Reverse Pareto Centroid → Pareto Centroid
Metric 1	↓-63.4%	↓-14.2%	↑+20.3%	↓-28.7%
Metric 3	↓-50.6%	↓-16.7%	↑+15.4%	↓-27.9%
Metric 4	↓-100.0%	↓-39.7%	↑+100.9%	↓-70.0%

Origamis Minimising and Maximising Individual Metrics

Origami Description	Origami Id	Scaffold Name	Rotation Offset	G Quad Staples	Metric 1	Metric 3	Metric 4	Origami Contact Map	Origami Sequences
Original Origami	703	original scaffold	703	2	233.27 ↓-11.1% 0.0%	11.02 ↑+6.6% 0.0%	1.06 ↓-48.5% 0.0%	CSV	FASTA
M1 Min Origami	221	original scaffold	221	2	138.92 ↓-47.1% ↓-40.4%	11.80 ↑+14.2% ↑+7.1%	2.10 ↑+2.5% ↑+98.8%	CSV	FASTA
M1 Max Origami	187	original scaffold	187	2	379.69 ↑+44.7% ↑+62.8%	11.80 ↑+14.2% ↑+7.1%	1.55 ↓-24.2% ↑+47.0%	CSV	FASTA
M3 Min Origami	688	original scaffold	688	3	274.24 ↑+4.5% ↑+17.6%	7.10 ↓-31.3% ↓-35.5%	1.85 ↓-9.6% ↑+75.5%	CSV	FASTA
M3 Max Origami	662	original scaffold	662	3	287.20 ↑+9.5% ↑+23.1%	14.39 ↑+39.2% ↑+30.6%	1.15 ↓-44.1% ↑+8.5%	CSV	FASTA
M4 Min Origami	179	original scaffold	179	3	246.54 ↓-6.0% ↑+5.7%	10.28 ↓-0.5% ↓-6.7%	0.00 ↓-100.0% ↓-100.0%	CSV	FASTA
M4 Max Origami	117	original scaffold	117	2	271.41 ↑+3.4% ↑+16.4%	8.02 ↓-22.4% ↓-27.2%	7.96 ↑+288.6% ↑+654.0%	CSV	FASTA

Worst Scoring Origamis (on Reverse Pareto Front)

SAW Top 5

SAW Rank	Origami Id	Scaffold Name	Rotation Offset	Metric 1	Metric 3	Metric 4	Origami Contact Map	Origami Sequences
1	53	original scaffold	53	279.56 ↑+6.5% ↑+19.8%	13.96 ↑+35.1% ↑+26.7%	7.19 ↑+251.0% ↑+581.1%	CSV	FASTA
2	54	original scaffold	54	261.80 ↓-0.2% ↑+12.2%	14.39 ↑+39.2% ↑+30.6%	7.19 ↑+251.0% ↑+581.1%	CSV	FASTA
3	464	original scaffold	464	313.24 ↑+19.4% ↑+34.3%	11.80 ↑+14.2% ↑+7.1%	6.69 ↑+226.9% ↑+534.3%	CSV	FASTA
4	369	original scaffold	369	310.73 ↑+18.4% ↑+33.2%	11.80 ↑+14.2% ↑+7.1%	5.82 ↑+184.4% ↑+451.9%	CSV	FASTA
5	370	original scaffold	370	328.98 ↑+25.4% ↑+41.0%	11.80 ↑+14.2% ↑+7.1%	4.45 ↑+117.1% ↑+321.4%	CSV	FASTA

KNEE Top 5

KNEE Rank	Origami Id	Scaffold Name	Rotation Offset	Metric 1	Metric 3	Metric 4	Origami Contact Map	Origami Sequences
1	53	original scaffold	53	279.56 ↑+6.5% ↑+19.8%	13.96 ↑+35.1% ↑+26.7%	7.19 ↑+251.0% ↑+581.1%	CSV	FASTA
2	464	original scaffold	464	313.24 ↑+19.4% ↑+34.3%	11.80 ↑+14.2% ↑+7.1%	6.69 ↑+226.9% ↑+534.3%	CSV	FASTA
3	54	original scaffold	54	261.80 ↓-0.2% ↑+12.2%	14.39 ↑+39.2% ↑+30.6%	7.19 ↑+251.0% ↑+581.1%	CSV	FASTA
4	369	original scaffold	369	310.73 ↑+18.4% ↑+33.2%	11.80 ↑+14.2% ↑+7.1%	5.82 ↑+184.4% ↑+451.9%	CSV	FASTA
5	370	original scaffold	370	328.98 ↑+25.4% ↑+41.0%	11.80 ↑+14.2% ↑+7.1%	4.45 ↑+117.1% ↑+321.4%	CSV	FASTA

TOPSIS Top 5

TOPSIS Rank	Origami Id	Scaffold Name	Rotation Offset	Metric 1	Metric 3	Metric 4	Origami Contact Map	Origami Sequences
1	53	original scaffold	53	279.56 ↑+6.5% ↑+19.8%	13.96 ↑+35.1% ↑+26.7%	7.19 ↑+251.0% ↑+581.1%	CSV	FASTA
2	54	original scaffold	54	261.80 ↓-0.2% ↑+12.2%	14.39 ↑+39.2% ↑+30.6%	7.19 ↑+251.0% ↑+581.1%	CSV	FASTA
3	464	original scaffold	464	313.24 ↑+19.4% ↑+34.3%	11.80 ↑+14.2% ↑+7.1%	6.69 ↑+226.9% ↑+534.3%	CSV	FASTA
4	369	original scaffold	369	310.73 ↑+18.4% ↑+33.2%	11.80 ↑+14.2% ↑+7.1%	5.82 ↑+184.4% ↑+451.9%	CSV	FASTA
5	370	original scaffold	370	328.98 ↑+25.4% ↑+41.0%	11.80 ↑+14.2% ↑+7.1%	4.45 ↑+117.1% ↑+321.4%	CSV	FASTA

Metric Score Pairwise Correlations

	Pearson's r	Metric 1	Metric 3	Metric 4
	Metric 1	1.00	0.05	-0.00
	Metric 3	0.05	1	0.00
	Metric 4	-0.00	0.00	1

	Spearman's r	Metric 1	Metric 3	Metric 4
	Metric 1	1	0.10	0.01
	Metric 3	0.10	1.00	0.04
	Metric 4	0.01	0.04	1

Metric Individual Execution Times

	Mean Execution Time (s)	Min Execution Time (s)	Max Execution Time (s)
Metric 1	0.2362	0.2276	0.3001
Metric 3	0.3018	0.2561	0.3576
Metric 4	0.0104	0.0089	0.0175

Whole Job Estimated Run Time on Single CPU

00:06:26