CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	PknotsRG		Vsfold5
MCC	0.552	>	0.426
Average MCC ± 95% Confidence Intervals	0.560 ± 0.066	>	0.446 ± 0.081
Sensitivity	0.492	>	0.359
Positive Predictive Value	0.625	>	0.512
Total TP	923	>	674
Total TN	338516	<	338677
Total FP	625	<	702
Total FP CONTRA	86	>	75
Total FP INCONS	468	<	567
Total FP COMP	71	>	60
Total FN	952	<	1201
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of PknotsRG and Vsfold5. 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 PknotsRG and Vsfold5).
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 PknotsRG and Vsfold5).
Comparison of average Matthews Correlation Coefficients (MCCs) for PknotsRG and Vsfold5. 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 PknotsRG and Vsfold5).

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Performance of PknotsRG - scored higher in this pairwise comparison

1. Total counts & total scores for PknotsRG

Total Base Pair Counts
Total TP	923
Total TN	338516
Total FP	625
Total FP CONTRA	86
Total FP INCONS	468
Total FP COMP	71
Total FN	952

Total Scores
MCC	0.552
Average MCC ± 95% Confidence Intervals	0.560 ± 0.066
Sensitivity	0.492
Positive Predictive Value	0.625
Nr of predictions	55

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2. Individual counts for PknotsRG [ 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...	0.95	0.91	1.00	10	396	0	0	0	0	1
2KFC_A	-	0.48	0.35	0.70	7	620	3	0	3	0	13
2KRL_A	-	0.72	0.60	0.86	24	5123	8	2	2	4	16
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LA5_A	-	0.39	0.26	0.63	5	622	3	1	2	0	14
2LC8_A	GP_knot1 links to Rfam database...	0.63	0.55	0.73	11	1525	4	1	3	0	9
2LKR_A	-	0.73	0.69	0.77	27	6070	8	2	6	0	12
2RP0_A	-	0.66	0.58	0.78	7	342	2	1	1	0	5
2WRQ_Y	tRNA links to Rfam database...	0.53	0.53	0.53	9	2833	13	5	3	5	8
2WW9_F	-	0.69	0.70	0.70	7	290	3	0	3	0	3
2WW9_D	-	0.14	0.12	0.19	3	1937	13	0	13	0	23
2WW9_E	-	0.53	0.29	1.00	4	557	0	0	0	0	10
2WWQ_V	tRNA links to Rfam database...	0.76	0.68	0.86	19	2904	5	0	3	2	9
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2ZZM_B	tRNA links to Rfam database...	0.21	0.19	0.25	6	3462	18	0	18	0	26
2ZZN_D	tRNA links to Rfam database...	0.84	0.78	0.91	21	2462	2	0	2	0	6
3A2K_C	tRNA links to Rfam database...	0.42	0.39	0.46	11	2902	13	2	11	0	17
3A3A_A	tRNA-Sec links to Rfam database...	0.87	0.76	1.00	28	3627	0	0	0	0	9
3ADB_C	-	0.33	0.32	0.36	12	4153	21	0	21	0	26
3AKZ_H	tRNA links to Rfam database...	0.41	0.39	0.44	11	2676	14	4	10	0	17
3AM1_B	-	0.68	0.63	0.73	22	3210	8	1	7	0	13
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3G4S_9	5S_rRNA links to Rfam database...	0.54	0.42	0.71	24	7347	10	1	9	0	33
3GCA_A	-	0.54	0.29	1.00	5	523	0	0	0	0	12
3GX2_A	SAM links to Rfam database...	0.67	0.55	0.81	22	4344	6	0	5	1	18
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IWN_A	c-di-GMP-I links to Rfam database...	0.20	0.18	0.24	6	4253	19	1	18	0	27
3IYQ_A	tmRNA links to Rfam database...	0.31	0.33	0.28	31	60617	80	24	54	2	63
3IZ4_A	tmRNA links to Rfam database...	0.51	0.47	0.55	62	70763	52	10	41	1	70
3IZF_C	5S_rRNA links to Rfam database...	0.59	0.52	0.67	28	6861	14	1	13	0	26
3J0L_2	-	0.24	0.24	0.24	8	6183	27	2	23	2	25
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_7	-	0.28	0.29	0.29	5	1208	12	0	12	0	12
3J0L_a	-	0.23	0.19	0.30	3	1118	7	1	6	0	13
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2828	22	1	21	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.31	0.30	0.32	10	12215	33	5	16	12	23
3JYX_3	5S_rRNA links to Rfam database...	0.62	0.63	0.61	17	6300	22	1	10	11	10
3KTW_C	-	0.77	0.65	0.90	28	4529	4	2	1	1	15
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NDB_M	-	0.77	0.69	0.86	42	9131	8	0	7	1	19
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3NPB_A	SAM links to Rfam database...	0.83	0.72	0.97	33	6987	3	0	1	2	13
3O58_2	5S_rRNA links to Rfam database...	0.59	0.61	0.58	23	7220	19	4	13	2	15
3O58_3	5_8S_rRNA links to Rfam database...	0.34	0.34	0.34	12	12368	34	2	21	11	23
3PDR_A	ykoK links to Rfam database...	0.75	0.63	0.90	45	12830	7	1	4	2	27
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	0.50	0.75	21	3888	7	1	6	0	21
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.48	0.38	0.61	14	3547	9	0	9	0	23
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.13	5	11742	43	5	29	9	28
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

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Performance of Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

Total Base Pair Counts
Total TP	674
Total TN	338677
Total FP	702
Total FP CONTRA	75
Total FP INCONS	567
Total FP COMP	60
Total FN	1201

Total Scores
MCC	0.426
Average MCC ± 95% Confidence Intervals	0.446 ± 0.081
Sensitivity	0.359
Positive Predictive Value	0.512
Nr of predictions	55

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2. Individual counts for Vsfold5 [ 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...	0.90	0.82	1.00	9	397	0	0	0	0	2
2KFC_A	-	0.48	0.35	0.70	7	620	3	0	3	0	13
2KRL_A	-	0.57	0.50	0.65	20	5120	11	5	6	0	20
2KX8_A	7SK links to Rfam database...	0.91	0.83	1.00	15	846	0	0	0	0	3
2LA5_A	-	-0.02	0.00	0.00	0	623	7	0	7	0	19
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1527	13	0	13	0	20
2LKR_A	-	0.27	0.23	0.32	9	6077	19	2	17	0	30
2RP0_A	-	0.64	0.42	1.00	5	346	0	0	0	0	7
2WRQ_Y	tRNA links to Rfam database...	0.53	0.53	0.53	9	2833	12	5	3	4	8
2WW9_F	-	0.59	0.60	0.60	6	290	4	0	4	0	4
2WW9_D	-	0.15	0.12	0.21	3	1939	11	1	10	0	23
2WW9_E	-	-0.01	0.00	0.00	0	556	5	0	5	0	14
2WWQ_V	tRNA links to Rfam database...	0.64	0.50	0.82	14	2909	4	0	3	1	14
2XQD_Y	tRNA links to Rfam database...	0.86	0.74	1.00	20	2830	0	0	0	0	7
2ZZM_B	tRNA links to Rfam database...	0.19	0.19	0.21	6	3458	22	1	21	0	26
2ZZN_D	tRNA links to Rfam database...	0.86	0.78	0.95	21	2463	1	0	1	0	6
3A2K_C	tRNA links to Rfam database...	0.84	0.71	1.00	20	2906	0	0	0	0	8
3A3A_A	tRNA-Sec links to Rfam database...	0.85	0.73	1.00	27	3628	0	0	0	0	10
3ADB_C	-	0.67	0.53	0.87	20	4163	3	0	3	0	18
3AKZ_H	tRNA links to Rfam database...	0.84	0.71	1.00	20	2681	0	0	0	0	8
3AM1_B	-	0.78	0.71	0.86	25	3211	4	1	3	0	10
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
3G4S_9	5S_rRNA links to Rfam database...	0.08	0.07	0.11	4	7344	33	0	33	0	53
3GCA_A	-	0.54	0.29	1.00	5	523	0	0	0	0	12
3GX2_A	SAM links to Rfam database...	0.51	0.40	0.67	16	4347	9	0	8	1	24
3IVN_B	Purine links to Rfam database...	0.76	0.58	1.00	18	2328	0	0	0	0	13
3IWN_A	c-di-GMP-I links to Rfam database...	0.25	0.21	0.30	7	4255	16	1	15	0	26
3IYQ_A	tmRNA links to Rfam database...	0.33	0.31	0.35	29	60642	61	15	40	6	65
3IZ4_A	tmRNA links to Rfam database...	0.29	0.24	0.36	32	70787	62	8	49	5	100
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.56	0.88	30	6869	4	0	4	0	24
3J0L_2	-	0.35	0.33	0.37	11	6186	21	3	16	2	22
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_a	-	0.39	0.31	0.50	5	1118	5	2	3	0	11
3J16_L	tRNA links to Rfam database...	0.82	0.67	1.00	20	2755	0	0	0	0	10
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2831	19	0	19	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.31	0.30	0.31	10	12214	32	3	19	10	23
3JYX_3	5S_rRNA links to Rfam database...	0.17	0.15	0.20	4	6308	18	4	12	2	23
3KTW_C	-	0.38	0.30	0.50	13	4534	13	3	10	0	30
3LA5_A	Purine links to Rfam database...	-0.01	0.00	0.00	0	2469	16	0	16	0	34
3NDB_M	-	0.06	0.05	0.08	3	9144	33	1	32	0	58
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3NPB_A	SAM links to Rfam database...	0.57	0.46	0.72	21	6992	9	1	7	1	25
3O58_2	5S_rRNA links to Rfam database...	0.45	0.42	0.48	16	7227	19	3	14	2	22
3O58_3	5_8S_rRNA links to Rfam database...	0.39	0.37	0.41	13	12371	28	7	12	9	22
3PDR_A	ykoK links to Rfam database...	0.57	0.44	0.74	32	12837	13	0	11	2	40
3RKF_A	Purine links to Rfam database...	0.75	0.65	0.88	22	2186	3	0	3	0	12
3SD1_A	THF links to Rfam database...	0.11	0.10	0.15	4	3890	22	0	22	0	38
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.16	0.14	0.20	5	3545	20	1	19	0	32
4A1C_3	5S_rRNA links to Rfam database...	0.26	0.22	0.32	12	7103	25	2	23	0	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.24	0.24	8	11748	37	3	22	12	25
4AOB_A	SAM links to Rfam database...	0.18	0.14	0.25	6	4347	19	1	17	1	36
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

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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 PknotsRG - scored higher in this pairwise comparison

1. Total counts & total scores for PknotsRG

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

Performance of Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

2. Individual counts for Vsfold5 [ download as .csv ]