CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAwolf		Vsfold5
MCC	0.518	>	0.505
Average MCC ± 95% Confidence Intervals	0.572 ± 0.092	<	0.579 ± 0.093
Sensitivity	0.524	>	0.518
Positive Predictive Value	0.526	>	0.506
Total TP	556	>	550
Total TN	74826	>	74796
Total FP	623	<	632
Total FP CONTRA	120	<	159
Total FP INCONS	381	>	378
Total FP COMP	122	>	95
Total FN	505	<	511
P-value	3.26115971074e-07

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Performance plots

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

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Performance of RNAwolf - scored higher in this pairwise comparison

1. Total counts & total scores for RNAwolf

Total Base Pair Counts
Total TP	556
Total TN	74826
Total FP	623
Total FP CONTRA	120
Total FP INCONS	381
Total FP COMP	122
Total FN	505

Total Scores
MCC	0.518
Average MCC ± 95% Confidence Intervals	0.572 ± 0.092
Sensitivity	0.524
Positive Predictive Value	0.526
Nr of predictions	58

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.52	0.50	0.56	9	512	7	0	7	0	9
2LDL_A	-	0.88	0.78	1.00	7	133	0	0	0	0	2
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LHP_A	-	1.00	1.00	1.00	15	246	1	0	0	1	0
2LI4_A	-	0.96	0.93	1.00	13	176	0	0	0	0	1
2LJJ_A	-	1.00	1.00	1.00	7	123	3	0	0	3	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.84	0.79	0.88	23	2414	11	0	3	8	6
2LU0_A	-	0.97	0.94	1.00	15	423	0	0	0	0	1
2LWK_A	-	0.48	0.45	0.56	5	198	5	0	4	1	6
2M58_A	-	0.60	0.58	0.64	7	533	4	1	3	0	5
2YIE_X	-	-0.01	0.00	0.00	0	536	11	1	7	3	7
2YIE_Z	-	0.62	0.63	0.63	5	594	7	1	2	4	3
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	8	0	5	3	4
3J0L_h	-	0.47	0.41	0.57	13	2117	12	1	9	2	19
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.14	0.18	0.14	2	397	13	4	8	1	9
3J0L_1	-	0.68	0.54	0.88	7	476	5	0	1	4	6
3J0L_7	-	-0.02	0.00	0.00	0	509	10	1	9	0	10
3J0L_g	-	-0.02	0.00	0.00	0	171	7	4	1	2	2
3J0L_2	-	0.14	0.15	0.15	4	2223	26	4	19	3	22
3J16_L	tRNA links to Rfam database...	0.58	0.57	0.60	12	1139	9	2	6	1	9
3J20_1	tRNA links to Rfam database...	0.53	0.55	0.52	11	1091	11	4	6	1	9
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	2	9	1	9
3J2C_O	-	0.41	0.44	0.40	18	3942	30	7	20	3	23
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.71	0.73	24	2987	13	1	8	4	10
3J3D_C	tRNA links to Rfam database...	0.92	0.95	0.90	18	948	3	2	0	1	1
3J3E_7	5S_rRNA links to Rfam database...	0.57	0.56	0.59	19	2709	15	1	12	2	15
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2719	37	6	17	14	15
3J3F_7	5S_rRNA links to Rfam database...	0.27	0.28	0.28	10	2898	27	4	22	1	26
3J3F_8	5_8S_rRNA links to Rfam database...	0.28	0.37	0.23	7	4730	39	9	15	15	12
3J3V_B	5S_rRNA links to Rfam database...	0.59	0.59	0.59	16	2629	16	1	10	5	11
3RKF_A	Purine links to Rfam database...	0.89	0.83	0.95	20	845	1	0	1	0	4
3SD1_A	THF links to Rfam database...	0.58	0.59	0.59	17	1504	12	2	10	0	12
3SIU_F	-	0.86	0.75	1.00	6	139	0	0	0	0	2
3SN2_B	IRE_II links to Rfam database...	1.00	1.00	1.00	12	142	0	0	0	0	0
3TRZ_Z	-	1.00	1.00	1.00	5	87	0	0	0	0	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	-0.05	0.00	0.00	0	103	6	0	5	1	5
3U4M_B	-	0.50	0.50	0.52	11	1255	12	1	9	2	11
3UZL_B	tRNA links to Rfam database...	0.93	0.88	1.00	14	1279	7	0	0	7	2
3VJR_D	-	1.00	1.00	1.00	12	239	1	0	0	1	0
3W3S_B	tRNA-Sec links to Rfam database...	0.70	0.70	0.72	23	1957	10	0	9	1	10
3ZEX_D	5S_rRNA links to Rfam database...	0.26	0.26	0.27	9	2763	24	8	16	0	26
3ZEX_E	-	-0.01	0.00	0.00	0	8244	60	23	37	0	34
3ZND_W	tRNA links to Rfam database...	0.67	0.75	0.60	6	1181	15	0	4	11	2
4A1C_3	5S_rRNA links to Rfam database...	0.32	0.30	0.35	11	2732	21	1	19	1	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.12	0.15	0.10	3	4487	38	12	14	12	17
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.26	0.24	0.30	7	1414	17	2	14	1	22
4ATO_G	-	-0.03	0.00	0.00	0	213	7	4	3	0	7
4ENB_A	crcB links to Rfam database...	0.45	0.40	0.55	6	461	5	1	4	0	9
4ENC_A	crcB links to Rfam database...	0.34	0.33	0.38	5	483	9	0	8	1	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.54	0.50	0.60	12	1182	8	3	5	0	12
4FRN_A	AdoCbl-variant links to Rfam database...	-0.01	0.00	0.00	0	1828	20	1	19	0	28
4JF2_A	preQ1-II links to Rfam database...	0.72	0.67	0.80	16	1062	4	4	0	0	8
4JRC_A	-	0.71	0.65	0.79	11	608	3	2	1	0	6

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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	550
Total TN	74796
Total FP	632
Total FP CONTRA	159
Total FP INCONS	378
Total FP COMP	95
Total FN	511

Total Scores
MCC	0.505
Average MCC ± 95% Confidence Intervals	0.579 ± 0.093
Sensitivity	0.518
Positive Predictive Value	0.506
Nr of predictions	58

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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
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	515	13	0	13	0	18
2LDL_A	-	0.94	0.89	1.00	8	132	1	0	0	1	1
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	7	123	3	0	0	3	0
2LK3_A	-	0.94	0.89	1.00	8	92	0	0	0	0	1
2LKR_A	-	0.31	0.31	0.32	9	2412	19	5	14	0	20
2LU0_A	-	0.68	0.63	0.77	10	425	3	0	3	0	6
2LWK_A	-	0.95	0.91	1.00	10	197	1	0	0	1	1
2M58_A	-	0.37	0.33	0.44	4	535	5	4	1	0	8
2YIE_X	-	0.43	0.57	0.33	4	532	10	2	6	2	3
2YIE_Z	-	-0.02	0.00	0.00	0	591	11	5	6	0	8
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	8	0	5	3	4
3J0L_h	-	0.20	0.19	0.24	6	2115	19	3	16	0	26
3J0L_8	-	0.74	0.57	1.00	4	72	0	0	0	0	3
3J0L_a	-	0.39	0.36	0.44	4	402	6	4	1	1	7
3J0L_1	-	0.25	0.23	0.30	3	474	8	3	4	1	10
3J0L_7	-	-0.02	0.00	0.00	0	506	13	3	10	0	10
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_2	-	0.42	0.42	0.44	11	2225	21	1	13	7	15
3J16_L	tRNA links to Rfam database...	0.98	0.95	1.00	20	1139	0	0	0	0	1
3J20_1	tRNA links to Rfam database...	0.75	0.75	0.75	15	1092	7	0	5	2	5
3J20_0	tRNA links to Rfam database...	0.76	0.76	0.76	16	1198	6	3	2	1	5
3J2C_O	-	0.33	0.32	0.36	13	3951	26	3	20	3	28
3J2L_3	5S_rRNA links to Rfam database...	0.70	0.71	0.71	24	2986	13	3	7	3	10
3J3D_C	tRNA links to Rfam database...	0.63	0.68	0.59	13	946	9	3	6	0	6
3J3E_7	5S_rRNA links to Rfam database...	0.60	0.59	0.63	20	2709	13	1	11	1	14
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.13	0.08	2	2718	31	10	12	9	13
3J3F_7	5S_rRNA links to Rfam database...	0.25	0.25	0.26	9	2900	25	4	21	0	27
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.47	0.27	9	4728	38	13	11	14	10
3J3V_B	5S_rRNA links to Rfam database...	0.18	0.19	0.19	5	2629	28	7	15	6	22
3RKF_A	Purine links to Rfam database...	0.90	0.92	0.88	22	841	3	3	0	0	2
3SD1_A	THF links to Rfam database...	0.13	0.14	0.15	4	1507	22	5	17	0	25
3SIU_F	-	0.86	0.75	1.00	6	139	0	0	0	0	2
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3TRZ_Z	-	1.00	1.00	1.00	5	87	1	0	0	1	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3UZL_B	tRNA links to Rfam database...	0.24	0.31	0.20	5	1268	20	9	11	0	11
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.83	0.85	0.82	28	1955	7	2	4	1	5
3ZEX_D	5S_rRNA links to Rfam database...	0.09	0.09	0.12	3	2771	24	5	17	2	32
3ZEX_E	-	0.11	0.15	0.09	5	8247	54	21	31	2	29
3ZND_W	tRNA links to Rfam database...	0.58	0.75	0.46	6	1178	17	4	3	10	2
4A1C_3	5S_rRNA links to Rfam database...	0.29	0.30	0.31	11	2727	26	4	21	1	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.28	8	4487	37	8	13	16	12
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.21	0.21	0.25	6	1413	19	2	16	1	23
4ATO_G	-	0.67	0.86	0.55	6	209	5	5	0	0	1
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...	0.60	0.58	0.64	14	1180	8	3	5	0	10
4FRN_A	AdoCbl-variant links to Rfam database...	0.15	0.14	0.17	4	1825	19	3	16	0	24
4JF2_A	preQ1-II links to Rfam database...	0.96	1.00	0.92	24	1056	2	2	0	0	0
4JRC_A	-	0.28	0.29	0.31	5	606	11	2	9	0	12

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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 RNAwolf - scored higher in this pairwise comparison

1. Total counts & total scores for RNAwolf

2. Individual counts for RNAwolf [ 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 ]