CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Vsfold4		RNAwolf
MCC	0.550	>	0.524
Average MCC ± 95% Confidence Intervals	0.620 ± 0.084	>	0.589 ± 0.090
Sensitivity	0.542	>	0.530
Positive Predictive Value	0.569	>	0.530
Total TP	592	>	579
Total TN	79729	>	79676
Total FP	548	<	641
Total FP CONTRA	121	<	132
Total FP INCONS	327	<	382
Total FP COMP	100	<	127
Total FN	500	<	513
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of Vsfold4 and RNAwolf. 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 Vsfold4 and RNAwolf).
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 Vsfold4 and RNAwolf).
Comparison of average Matthews Correlation Coefficients (MCCs) for Vsfold4 and RNAwolf. 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 Vsfold4 and RNAwolf).

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Performance of Vsfold4 - scored higher in this pairwise comparison

1. Total counts & total scores for Vsfold4

Total Base Pair Counts
Total TP	592
Total TN	79729
Total FP	548
Total FP CONTRA	121
Total FP INCONS	327
Total FP COMP	100
Total FN	500

Total Scores
MCC	0.550
Average MCC ± 95% Confidence Intervals	0.620 ± 0.084
Sensitivity	0.542
Positive Predictive Value	0.569
Nr of predictions	60

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2. Individual counts for Vsfold4 [ 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	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.35	0.38	0.34	11	2408	21	7	14	0	18
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
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	-	-0.02	0.00	0.00	0	538	6	0	6	0	12
2YIE_X	-	0.53	0.57	0.50	4	536	6	1	3	2	3
2YIE_Z	-	-0.02	0.00	0.00	0	591	11	5	6	0	8
3AMU_B	tRNA links to Rfam database...	0.73	0.74	0.74	14	1138	8	0	5	3	5
3J0L_h	-	0.44	0.38	0.52	12	2117	11	2	9	0	20
3J0L_7	-	0.69	0.70	0.70	7	509	4	1	2	1	3
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_8	-	0.74	0.57	1.00	4	72	0	0	0	0	3
3J0L_1	-	0.26	0.23	0.33	3	475	7	2	4	1	10
3J0L_a	-	0.39	0.36	0.44	4	402	6	4	1	1	7
3J0L_2	-	0.47	0.46	0.50	12	2226	18	1	11	6	14
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...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J2C_O	-	0.33	0.32	0.36	13	3951	26	3	20	3	28
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.71	0.73	24	2987	12	3	6	3	10
3J3D_C	tRNA links to Rfam database...	0.48	0.53	0.45	10	946	12	4	8	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.13	0.09	2	2720	32	9	11	12	13
3J3E_7	5S_rRNA links to Rfam database...	0.61	0.56	0.68	19	2713	10	1	8	1	15
3J3F_7	5S_rRNA links to Rfam database...	0.25	0.25	0.26	9	2900	25	6	19	0	27
3J3F_8	5_8S_rRNA links to Rfam database...	0.35	0.42	0.30	8	4734	30	11	8	11	11
3J3V_B	5S_rRNA links to Rfam database...	0.19	0.19	0.22	5	2633	24	3	15	6	22
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...	0.23	0.24	0.24	7	1504	22	5	17	0	22
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...	0.66	0.69	0.65	11	1276	10	3	3	4	5
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.74	0.70	0.79	23	1960	7	1	5	1	10
3ZEX_G	-	0.31	0.29	0.34	13	6469	31	5	20	6	32
3ZEX_D	5S_rRNA links to Rfam database...	0.66	0.63	0.71	22	2765	10	4	5	1	13
3ZEX_E	-	0.12	0.15	0.11	5	8259	40	13	27	0	29
3ZND_W	tRNA links to Rfam database...	0.58	0.75	0.46	6	1178	17	4	3	10	2
4A1C_2	5_8S_rRNA links to Rfam database...	0.36	0.40	0.33	8	4492	28	4	12	12	12
4A1C_3	5S_rRNA links to Rfam database...	0.29	0.30	0.31	11	2727	26	4	21	1	26
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ATO_G	-	0.38	0.43	0.38	3	212	5	5	0	0	4
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...	0.77	0.60	1.00	9	487	0	0	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.60	0.58	0.64	14	1180	8	3	5	0	10
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0
4JF2_A	preQ1-II links to Rfam database...	0.74	0.67	0.84	16	1063	3	0	3	0	8
4JRC_A	-	0.34	0.29	0.42	5	610	7	0	7	0	12

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Performance of RNAwolf - scored lower in this pairwise comparison

1. Total counts & total scores for RNAwolf

Total Base Pair Counts
Total TP	579
Total TN	79676
Total FP	641
Total FP CONTRA	132
Total FP INCONS	382
Total FP COMP	127
Total FN	513

Total Scores
MCC	0.524
Average MCC ± 95% Confidence Intervals	0.589 ± 0.090
Sensitivity	0.530
Positive Predictive Value	0.530
Nr of predictions	60

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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
2LQZ_A	-	1.00	1.00	1.00	8	124	1	0	0	1	0
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_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_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_1	-	0.68	0.54	0.88	7	476	5	0	1	4	6
3J0L_a	-	0.14	0.18	0.14	2	397	13	4	8	1	9
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_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2719	37	6	17	14	15
3J3E_7	5S_rRNA links to Rfam database...	0.57	0.56	0.59	19	2709	15	1	12	2	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_G	-	0.20	0.20	0.21	9	6465	37	13	20	4	36
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_2	5_8S_rRNA links to Rfam database...	0.12	0.15	0.10	3	4487	38	12	14	12	17
4A1C_3	5S_rRNA links to Rfam database...	0.32	0.30	0.35	11	2732	21	1	19	1	26
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
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0
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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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 Vsfold4 - scored higher in this pairwise comparison

1. Total counts & total scores for Vsfold4

2. Individual counts for Vsfold4 [ download as .csv ]

Performance of RNAwolf - scored lower in this pairwise comparison

1. Total counts & total scores for RNAwolf

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