CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	IPknot		CentroidFold
MCC	0.669	>	0.627
Average MCC ± 95% Confidence Intervals	0.721 ± 0.075	>	0.707 ± 0.076
Sensitivity	0.645	>	0.613
Positive Predictive Value	0.695	>	0.644
Total TP	1335	>	1268
Total TN	976182	>	976134
Total FP	829	<	925
Total FP CONTRA	162	<	185
Total FP INCONS	424	<	516
Total FP COMP	243	>	224
Total FN	734	<	801
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of IPknot and CentroidFold. 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 IPknot and CentroidFold).
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 IPknot and CentroidFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for IPknot and CentroidFold. 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 IPknot and CentroidFold).

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Performance of IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP	1335
Total TN	976182
Total FP	829
Total FP CONTRA	162
Total FP INCONS	424
Total FP COMP	243
Total FN	734

Total Scores
MCC	0.669
Average MCC ± 95% Confidence Intervals	0.721 ± 0.075
Sensitivity	0.645
Positive Predictive Value	0.695
Nr of predictions	69

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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
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.41	0.33	0.55	6	517	5	1	4	0	12
2LDL_A	-	1.00	1.00	1.00	9	131	0	0	0	0	0
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	-	0.88	0.86	0.89	25	2412	9	0	3	6	4
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LU0_A	-	1.00	1.00	1.00	16	422	0	0	0	0	0
2LWK_A	-	0.95	0.91	1.00	10	197	1	0	0	1	1
2M58_A	-	0.71	0.58	0.88	7	536	1	1	0	0	5
2YIE_Z	-	0.53	0.63	0.45	5	591	6	4	2	0	3
2YIE_X	-	1.00	1.00	1.00	7	537	3	0	0	3	0
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.16	0.18	0.18	2	400	10	3	6	1	9
3J0L_1	-	0.83	0.77	0.91	10	473	4	0	1	3	3
3J0L_h	-	0.90	0.81	1.00	26	2114	2	0	0	2	6
3J0L_7	-	-0.02	0.00	0.00	0	512	7	1	6	0	10
3J0L_2	-	0.49	0.46	0.52	12	2227	18	0	11	7	14
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	0	0	0	0	4
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.75	0.74	0.76	305	421966	159	17	80	62	107
3J2C_O	-	0.98	0.95	1.00	39	3948	4	0	0	4	2
3J2C_M	-	0.72	0.74	0.71	71	39825	58	13	16	29	25
3J2L_3	5S_rRNA links to Rfam database...	0.82	0.82	0.82	28	2986	10	0	6	4	6
3J3D_C	tRNA links to Rfam database...	0.52	0.53	0.53	10	949	9	3	6	0	9
3J3E_7	5S_rRNA links to Rfam database...	0.60	0.56	0.66	19	2712	11	1	9	1	15
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2723	25	5	14	6	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.47	0.28	9	4729	40	11	12	17	10
3J3F_7	5S_rRNA links to Rfam database...	0.81	0.83	0.79	30	2896	10	1	7	2	6
3J3V_B	5S_rRNA links to Rfam database...	0.54	0.56	0.54	15	2628	16	4	9	3	12
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...	0.74	0.69	0.80	20	1508	5	0	5	0	9
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	-	0.91	0.91	0.91	20	1254	3	2	0	1	2
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	0	0	0	0	0
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.94	0.91	0.97	30	1958	2	0	1	1	3
3ZEX_H	-	0.28	0.37	0.22	7	3593	25	15	10	0	12
3ZEX_F	-	0.00	0.00	0.00	0	910	9	0	4	5	4
3ZEX_C	5_8S_rRNA links to Rfam database...	0.51	0.34	0.77	10	5361	7	1	2	4	19
3ZEX_G	-	0.89	0.91	0.87	41	6460	18	5	1	12	4
3ZEX_E	-	0.00	0.00	0.00	0	8256	53	19	29	5	34
3ZEX_D	5S_rRNA links to Rfam database...	0.81	0.80	0.82	28	2762	10	0	6	4	7
3ZEX_B	-	0.33	0.27	0.40	95	421115	160	26	116	18	251
3ZND_W	tRNA links to Rfam database...	0.24	0.38	0.16	3	1172	25	9	7	9	5
4A1C_3	5S_rRNA links to Rfam database...	0.83	0.81	0.86	30	2728	7	0	5	2	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.25	0.22	5	4493	26	8	10	8	15
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	-	0.49	0.57	0.44	4	211	6	0	5	1	3
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...	0.59	0.53	0.67	8	484	4	0	4	0	7
4FNJ_A	-	0.91	0.83	1.00	10	240	0	0	0	0	2
4FRG_B	AdoCbl-variant links to Rfam database...	0.75	0.71	0.81	17	1181	4	3	1	0	7
4FRN_A	AdoCbl-variant links to Rfam database...	0.79	0.71	0.87	20	1825	3	1	2	0	8
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0
4JF2_A	preQ1-II links to Rfam database...	0.96	0.96	0.96	23	1058	1	1	0	0	1
4JRC_A	-	0.45	0.29	0.71	5	615	2	0	2	0	12

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Performance of CentroidFold - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidFold

Total Base Pair Counts
Total TP	1268
Total TN	976134
Total FP	925
Total FP CONTRA	185
Total FP INCONS	516
Total FP COMP	224
Total FN	801

Total Scores
MCC	0.627
Average MCC ± 95% Confidence Intervals	0.707 ± 0.076
Sensitivity	0.613
Positive Predictive Value	0.644
Nr of predictions	69

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2. Individual counts for CentroidFold [ 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...	0.51	0.39	0.70	7	518	3	1	2	0	11
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
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	-	0.88	0.86	0.89	25	2412	8	0	3	5	4
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LU0_A	-	0.93	0.88	1.00	14	424	0	0	0	0	2
2LWK_A	-	1.00	1.00	1.00	11	196	1	0	0	1	0
2M58_A	-	-0.02	0.00	0.00	0	538	6	0	6	0	12
2YIE_Z	-	0.53	0.63	0.45	5	591	6	4	2	0	3
2YIE_X	-	1.00	1.00	1.00	7	537	3	0	0	3	0
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3J0L_g	-	0.00	0.00	0.00	0	176	0	0	0	0	2
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.41	0.36	0.50	4	403	5	3	1	1	7
3J0L_1	-	0.73	0.62	0.89	8	475	3	0	1	2	5
3J0L_h	-	0.89	0.88	0.90	28	2109	5	0	3	2	4
3J0L_7	-	-0.01	0.00	0.00	0	514	5	1	4	0	10
3J0L_2	-	0.28	0.31	0.28	8	2221	24	2	19	3	18
3J16_L	tRNA links to Rfam database...	0.59	0.57	0.63	12	1140	7	0	7	0	9
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	2	0	0	2	0
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.70	0.69	0.70	286	421962	177	23	97	57	126
3J2C_O	-	0.95	0.90	1.00	37	3950	6	0	0	6	4
3J2C_M	-	0.60	0.60	0.60	58	39829	58	14	24	20	38
3J2L_3	5S_rRNA links to Rfam database...	0.74	0.76	0.72	26	2984	15	1	9	5	8
3J3D_C	tRNA links to Rfam database...	0.73	0.79	0.68	15	946	7	3	4	0	4
3J3E_7	5S_rRNA links to Rfam database...	0.61	0.59	0.65	20	2710	13	2	9	2	14
3J3E_8	5_8S_rRNA links to Rfam database...	0.12	0.13	0.13	2	2726	22	4	10	8	13
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.47	0.28	9	4729	37	12	11	14	10
3J3F_7	5S_rRNA links to Rfam database...	0.84	0.86	0.82	31	2896	9	1	6	2	5
3J3V_B	5S_rRNA links to Rfam database...	0.72	0.74	0.71	20	2628	16	1	7	8	7
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...	0.70	0.69	0.71	20	1505	8	4	4	0	9
3SIU_F	-	0.93	0.88	1.00	7	138	0	0	0	0	1
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	-	0.81	0.77	0.85	17	1256	5	0	3	2	5
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	0	0	0	0	0
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.95	0.91	1.00	30	1959	1	0	0	1	3
3ZEX_H	-	0.27	0.37	0.21	7	3591	27	16	11	0	12
3ZEX_F	-	0.00	0.00	0.00	0	910	9	0	4	5	4
3ZEX_C	5_8S_rRNA links to Rfam database...	0.48	0.34	0.67	10	5359	6	1	4	1	19
3ZEX_G	-	0.45	0.44	0.47	20	6464	32	6	17	9	25
3ZEX_E	-	0.00	0.00	0.00	0	8255	51	19	30	2	34
3ZEX_D	5S_rRNA links to Rfam database...	0.88	0.86	0.91	30	2763	8	0	3	5	5
3ZEX_B	-	0.27	0.25	0.31	85	421074	210	38	155	17	261
3ZND_W	tRNA links to Rfam database...	0.24	0.38	0.16	3	1172	25	9	7	9	5
4A1C_3	5S_rRNA links to Rfam database...	0.80	0.78	0.83	29	2728	8	0	6	2	8
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.19	5	4490	29	9	12	8	15
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	-	0.61	0.57	0.67	4	214	2	0	2	0	3
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	1	0	0	1	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	1	0	0	1	4
4FNJ_A	-	0.91	0.83	1.00	10	240	0	0	0	0	2
4FRG_B	AdoCbl-variant links to Rfam database...	0.75	0.71	0.81	17	1181	4	3	1	0	7
4FRN_A	AdoCbl-variant links to Rfam database...	0.80	0.71	0.91	20	1826	2	1	1	0	8
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5
4JRC_A	-	0.38	0.41	0.39	7	604	11	0	11	0	10

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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 IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

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

Performance of CentroidFold - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidFold

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