CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

Home

Methods

Datasets

Rankings

RNA 2D Atlas

Help

FAQ

Contact us

RSS feeds

Twitter

Overview

Metric	TurboFold(20)		IPknot
MCC	0.764	>	0.712
Average MCC ± 95% Confidence Intervals	0.759 ± 0.117	>	0.707 ± 0.119
Sensitivity	0.726	>	0.678
Positive Predictive Value	0.810	>	0.756
Total TP	255	>	238
Total TN	27648	=	27648
Total FP	88	<	105
Total FP CONTRA	15	<	18
Total FP INCONS	45	<	59
Total FP COMP	28	=	28
Total FN	96	<	113
P-value	2.04409141234e-08

^top

Performance plots

Comparison of performance of TurboFold(20) and IPknot. Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for TurboFold(20) and IPknot).
Comparison of performance of TurboFold(20) and IPknot. Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for TurboFold(20) and IPknot).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for TurboFold(20) and IPknot).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for TurboFold(20) and IPknot).
Comparison of average Matthews Correlation Coefficients (MCCs) for TurboFold(20) and IPknot. The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for TurboFold(20) and IPknot).
Comparison of average Matthews Correlation Coefficients (MCCs) for TurboFold(20) and IPknot. The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for TurboFold(20) and IPknot).

^top

Performance of TurboFold(20) - scored higher in this pairwise comparison

1. Total counts & total scores for TurboFold(20)

Total Base Pair Counts
Total TP	255
Total TN	27648
Total FP	88
Total FP CONTRA	15
Total FP INCONS	45
Total FP COMP	28
Total FN	96

Total Scores
MCC	0.764
Average MCC ± 95% Confidence Intervals	0.759 ± 0.117
Sensitivity	0.726
Positive Predictive Value	0.810
Nr of predictions	14

^top

2. Individual counts for TurboFold(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	1	5	1	5
3J2L_3	5S_rRNA links to Rfam database...	0.92	0.91	0.94	31	2987	5	1	1	3	3
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.71	0.69	0.74	20	1506	7	2	5	0	9
3ZEX_C	5_8S_rRNA links to Rfam database...	0.49	0.45	0.54	13	5350	15	2	9	4	16
3ZEX_D	5S_rRNA links to Rfam database...	0.86	0.80	0.93	28	2766	6	0	2	4	7
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.84	0.89	31	2728	6	0	4	2	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.21	5	4492	28	6	13	9	15
4AOB_A	SAM links to Rfam database...	0.67	0.59	0.77	17	1415	6	2	3	1	12
4ENB_A	crcB links to Rfam database...	0.77	0.60	1.00	9	463	0	0	0	0	6
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.93	0.88	1.00	21	1181	0	0	0	0	3

^top

Performance of IPknot - scored lower in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP	238
Total TN	27648
Total FP	105
Total FP CONTRA	18
Total FP INCONS	59
Total FP COMP	28
Total FN	113

Total Scores
MCC	0.712
Average MCC ± 95% Confidence Intervals	0.707 ± 0.119
Sensitivity	0.678
Positive Predictive Value	0.756
Nr of predictions	14

^top

2. Individual counts for IPknot [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J2L_3	5S_rRNA links to Rfam database...	0.82	0.82	0.82	28	2986	10	0	6	4	6
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.74	0.69	0.80	20	1508	5	0	5	0	9
3ZEX_C	5_8S_rRNA links to Rfam database...	0.51	0.34	0.77	10	5361	7	1	2	4	19
3ZEX_D	5S_rRNA links to Rfam database...	0.81	0.80	0.82	28	2762	10	0	6	4	7
4A1C_3	5S_rRNA links to Rfam database...	0.83	0.81	0.86	30	2728	7	0	5	2	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.25	0.22	5	4493	26	8	10	8	15
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.59	0.53	0.67	8	484	4	0	4	0	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.75	0.71	0.81	17	1181	4	3	1	0	7

^top

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.

Table of contents:

Overview

Performance plots

Performance of TurboFold(20) - scored higher in this pairwise comparison

1. Total counts & total scores for TurboFold(20)

2. Individual counts for TurboFold(20) [ download as .csv ]

Performance of IPknot - scored lower in this pairwise comparison

1. Total counts & total scores for IPknot

2. Individual counts for IPknot [ download as .csv ]