CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	TurboFold(20)		IPknot
MCC	0.643	>	0.601
Average MCC ± 95% Confidence Intervals	0.652 ± 0.109	>	0.609 ± 0.114
Sensitivity	0.515	>	0.485
Positive Predictive Value	0.809	>	0.751
Total TP	262	>	247
Total TN	73053	>	73048
Total FP	81	<	96
Total FP CONTRA	5	<	8
Total FP INCONS	57	<	74
Total FP COMP	19	>	14
Total FN	247	<	262
P-value	2.1413769576e-08

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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).

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

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

Total Base Pair Counts
Total TP	262
Total TN	73053
Total FP	81
Total FP CONTRA	5
Total FP INCONS	57
Total FP COMP	19
Total FN	247

Total Scores
MCC	0.643
Average MCC ± 95% Confidence Intervals	0.652 ± 0.109
Sensitivity	0.515
Positive Predictive Value	0.809
Nr of predictions	14

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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...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_0	tRNA links to Rfam database...	0.66	0.57	0.77	17	2828	6	0	5	1	13
3J2L_3	5S_rRNA links to Rfam database...	0.74	0.58	0.94	31	7842	5	0	2	3	22
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.59	0.48	0.74	20	3889	7	1	6	0	22
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.27	0.56	14	14171	14	2	9	3	38
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.63	0.91	31	6987	3	0	3	0	18
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	0	6	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.21	5	11757	28	0	19	9	28
4AOB_A	SAM links to Rfam database...	0.56	0.40	0.77	17	4349	6	1	4	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.81	0.66	1.00	21	3465	0	0	0	0	11

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Performance of IPknot - scored lower in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP	247
Total TN	73048
Total FP	96
Total FP CONTRA	8
Total FP INCONS	74
Total FP COMP	14
Total FN	262

Total Scores
MCC	0.601
Average MCC ± 95% Confidence Intervals	0.609 ± 0.114
Sensitivity	0.485
Positive Predictive Value	0.751
Nr of predictions	14

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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...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_0	tRNA links to Rfam database...	0.45	0.40	0.52	12	2827	12	0	11	1	18
3J2L_3	5S_rRNA links to Rfam database...	0.66	0.55	0.81	29	7839	9	0	7	2	24
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.61	0.48	0.80	20	3891	5	0	5	0	22
3ZEX_C	5_8S_rRNA links to Rfam database...	0.41	0.21	0.79	11	14182	6	1	2	3	41
3ZEX_D	5S_rRNA links to Rfam database...	0.72	0.63	0.82	31	6983	7	0	7	0	18
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	1	5	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	11755	26	4	17	5	28
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.52	0.42	0.67	8	1314	4	0	4	0	11
4FRG_B	AdoCbl-variant links to Rfam database...	0.69	0.56	0.86	18	3465	3	1	2	0	14

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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 ]