CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	MXScarna(20)		HotKnots
MCC	0.755	>	0.668
Average MCC ± 95% Confidence Intervals	0.762 ± 0.067	>	0.703 ± 0.100
Sensitivity	0.720	>	0.692
Positive Predictive Value	0.796	>	0.651
Total TP	645	>	620
Total TN	92052	>	91910
Total FP	335	<	476
Total FP CONTRA	65	<	105
Total FP INCONS	100	<	227
Total FP COMP	170	>	144
Total FN	251	<	276
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of MXScarna(20) and HotKnots. 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 MXScarna(20) and HotKnots).
Comparison of performance of MXScarna(20) and HotKnots. 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 MXScarna(20) and HotKnots).
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 MXScarna(20) and HotKnots).
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 MXScarna(20) and HotKnots).
Comparison of average Matthews Correlation Coefficients (MCCs) for MXScarna(20) and HotKnots. 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 MXScarna(20) and HotKnots).
Comparison of average Matthews Correlation Coefficients (MCCs) for MXScarna(20) and HotKnots. 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 MXScarna(20) and HotKnots).

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

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

Total Base Pair Counts
Total TP	645
Total TN	92052
Total FP	335
Total FP CONTRA	65
Total FP INCONS	100
Total FP COMP	170
Total FN	251

Total Scores
MCC	0.755
Average MCC ± 95% Confidence Intervals	0.762 ± 0.067
Sensitivity	0.720
Positive Predictive Value	0.796
Nr of predictions	34

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	1.00	1.00	1.00	10	164	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	0.73	0.72	0.76	13	340	5	0	4	1	5
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	14	0	0	14	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.60	0.36	1.00	4	1831	3	0	0	3	7
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.88	0.86	0.91	30	2012	4	0	3	1	5
3A2K_C	tRNA links to Rfam database...	0.74	0.73	0.76	16	1087	6	1	4	1	6
3AMU_B	tRNA links to Rfam database...	1.00	1.00	1.00	19	1138	3	0	0	3	0
3G4S_9	5S_rRNA links to Rfam database...	0.78	0.77	0.80	20	2711	16	2	3	11	6
3GX2_A	SAM links to Rfam database...	0.81	0.79	0.85	22	1423	6	2	2	2	6
3IVN_B	Purine links to Rfam database...	0.81	0.74	0.89	17	884	2	2	0	0	6
3IZ4_A	tmRNA links to Rfam database...	0.58	0.54	0.63	51	25455	35	18	12	5	44
3IZF_C	5S_rRNA links to Rfam database...	0.87	0.89	0.86	31	2604	12	0	5	7	4
3J20_0	tRNA links to Rfam database...	0.93	0.90	0.95	19	1199	1	1	0	0	2
3J20_1	tRNA links to Rfam database...	0.97	0.95	1.00	19	1093	1	0	0	1	1
3J2L_3	5S_rRNA links to Rfam database...	0.67	0.65	0.71	22	2989	11	3	6	2	12
3JYV_7	tRNA links to Rfam database...	0.95	0.90	1.00	18	1093	2	0	0	2	2
3JYX_4	5_8S_rRNA links to Rfam database...	0.70	0.83	0.59	10	4739	32	5	2	25	2
3JYX_3	5S_rRNA links to Rfam database...	0.73	0.73	0.73	11	2363	26	0	4	22	4
3LA5_A	Purine links to Rfam database...	0.87	0.80	0.95	20	933	1	1	0	0	5
3NPB_A	SAM links to Rfam database...	0.77	0.73	0.82	27	2245	9	2	4	3	10
3O58_2	5S_rRNA links to Rfam database...	0.92	0.90	0.93	28	2724	13	0	2	11	3
3O58_3	5_8S_rRNA links to Rfam database...	0.62	0.59	0.65	13	4744	18	5	2	11	9
3PDR_A	ykoK links to Rfam database...	0.85	0.82	0.89	41	4794	9	2	3	4	9
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.74	0.76	0.73	22	1503	9	6	2	1	7
3ZEX_C	5_8S_rRNA links to Rfam database...	0.35	0.31	0.41	9	5352	15	3	10	2	20
3ZEX_D	5S_rRNA links to Rfam database...	0.85	0.83	0.88	29	2763	13	0	4	9	6
4A1C_3	5S_rRNA links to Rfam database...	0.80	0.78	0.83	29	2728	12	0	6	6	8
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.21	5	4492	36	8	11	17	15
4AOB_A	SAM links to Rfam database...	0.68	0.69	0.69	20	1408	13	2	7	4	9
4ENB_A	crcB links to Rfam database...	0.29	0.13	0.67	2	469	1	0	1	0	13
4ENC_A	crcB links to Rfam database...	0.68	0.47	1.00	7	489	0	0	0	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.65	0.58	0.74	14	1183	6	2	3	1	10

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Performance of HotKnots - scored lower in this pairwise comparison

1. Total counts & total scores for HotKnots

Total Base Pair Counts
Total TP	620
Total TN	91910
Total FP	476
Total FP CONTRA	105
Total FP INCONS	227
Total FP COMP	144
Total FN	276

Total Scores
MCC	0.668
Average MCC ± 95% Confidence Intervals	0.703 ± 0.100
Sensitivity	0.692
Positive Predictive Value	0.651
Nr of predictions	34

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	1.00	1.00	1.00	10	164	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	14	0	0	14	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	25	0	6	19	3
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.35	0.34	0.38	12	2013	21	1	19	1	23
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3G4S_9	5S_rRNA links to Rfam database...	0.78	0.77	0.80	20	2711	14	2	3	9	6
3GX2_A	SAM links to Rfam database...	0.81	0.79	0.85	22	1423	5	2	2	1	6
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IZ4_A	tmRNA links to Rfam database...	0.56	0.60	0.52	57	25426	57	26	27	4	38
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	9	0	5	4	3
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J20_1	tRNA links to Rfam database...	0.75	0.75	0.75	15	1092	8	0	5	3	5
3J2L_3	5S_rRNA links to Rfam database...	0.80	0.82	0.78	28	2984	12	1	7	4	6
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1089	22	4	18	0	20
3JYX_4	5_8S_rRNA links to Rfam database...	0.61	0.83	0.45	10	4734	31	10	2	19	2
3JYX_3	5S_rRNA links to Rfam database...	0.77	0.80	0.75	12	2362	27	0	4	23	3
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NPB_A	SAM links to Rfam database...	0.85	0.78	0.94	29	2247	6	0	2	4	8
3O58_2	5S_rRNA links to Rfam database...	0.87	0.87	0.87	27	2723	12	0	4	8	4
3O58_3	5_8S_rRNA links to Rfam database...	0.26	0.36	0.19	8	4722	35	16	18	1	14
3PDR_A	ykoK links to Rfam database...	0.81	0.80	0.82	40	4791	11	3	6	2	10
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...	0.77	0.76	0.79	22	1505	6	4	2	0	7
3ZEX_C	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	5328	46	11	35	0	29
3ZEX_D	5S_rRNA links to Rfam database...	0.90	0.86	0.94	30	2764	6	0	2	4	5
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	7	0	4	3	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	42	12	16	14	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FRG_B	AdoCbl-variant links to Rfam database...	0.36	0.38	0.38	9	1178	15	2	13	0	15

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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 MXScarna(20) - scored higher in this pairwise comparison

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

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

Performance of HotKnots - scored lower in this pairwise comparison

1. Total counts & total scores for HotKnots

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