CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAsubopt		RDfolder
MCC	0.790	>	0.677
Average MCC ± 95% Confidence Intervals	0.785 ± 0.064	>	0.692 ± 0.073
Sensitivity	0.790	>	0.637
Positive Predictive Value	0.801	>	0.735
Total TP	1088	>	878
Total TN	53446	<	53610
Total FP	387	>	383
Total FP CONTRA	66	<	75
Total FP INCONS	205	<	242
Total FP COMP	116	>	66
Total FN	290	<	500
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of RNAsubopt and RDfolder. 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 RNAsubopt and RDfolder).
Comparison of performance of RNAsubopt and RDfolder. 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 RNAsubopt and RDfolder).
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 RNAsubopt and RDfolder).
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 RNAsubopt and RDfolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAsubopt and RDfolder. 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 RNAsubopt and RDfolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAsubopt and RDfolder. 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 RNAsubopt and RDfolder).

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Performance of RNAsubopt - scored higher in this pairwise comparison

1. Total counts & total scores for RNAsubopt

Total Base Pair Counts
Total TP	1088
Total TN	53446
Total FP	387
Total FP CONTRA	66
Total FP INCONS	205
Total FP COMP	116
Total FN	290

Total Scores
MCC	0.790
Average MCC ± 95% Confidence Intervals	0.785 ± 0.064
Sensitivity	0.790
Positive Predictive Value	0.801
Nr of predictions	96

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2K5Z_A	-	0.95	0.91	1.00	10	176	0	0	0	0	1
2K63_A	-	0.94	0.89	1.00	8	160	0	0	0	0	1
2K66_A	-	1.00	1.00	1.00	9	80	0	0	0	0	0
2KD8_A	-	0.87	0.78	1.00	7	101	0	0	0	0	2
2KDQ_B	mir-TAR links to Rfam database...	1.00	1.00	1.00	10	164	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	0.88	0.89	0.89	16	449	3	0	2	1	2
2KEZ_A	-	1.00	1.00	1.00	8	94	0	0	0	0	0
2KFC_A	-	-0.03	0.00	0.00	0	229	7	1	6	0	8
2KGP_A	-	1.00	1.00	1.00	9	112	0	0	0	0	0
2KMJ_A	-	1.00	1.00	1.00	11	157	0	0	0	0	0
2KPV_A	-	0.96	0.92	1.00	12	201	0	0	0	0	1
2KU0_A	-	0.96	0.92	1.00	11	281	0	0	0	0	1
2KUR_A	K10_TLS links to Rfam database...	0.89	0.89	0.89	17	448	2	0	2	0	2
2KUU_A	K10_TLS links to Rfam database...	0.88	0.89	0.89	16	429	3	0	2	1	2
2KUV_A	K10_TLS links to Rfam database...	0.89	0.89	0.89	17	420	2	0	2	0	2
2KUW_A	K10_TLS links to Rfam database...	0.94	0.94	0.94	17	452	2	0	1	1	1
2KX8_A	7SK links to Rfam database...	0.97	0.94	1.00	15	356	0	0	0	0	1
2KXM_A	-	1.00	1.00	1.00	8	141	0	0	0	0	0
2KZL_A	-	1.00	1.00	1.00	13	507	1	0	0	1	0
2L1F_A	Gammaretro_CES links to Rfam database...	0.95	0.91	1.00	21	742	0	0	0	0	2
2L1F_B	Gammaretro_CES links to Rfam database...	0.96	0.92	1.00	22	769	0	0	0	0	2
2L2K_A	-	1.00	1.00	1.00	17	332	0	0	0	0	0
2L3C_B	-	0.96	0.93	1.00	13	226	0	0	0	0	1
2L3E_A	-	1.00	1.00	1.00	12	228	1	0	0	1	0
2L3J_B	mir-2985-2 links to Rfam database...	1.00	1.00	1.00	30	955	0	0	0	0	0
2L5Z_A	-	1.00	1.00	1.00	9	102	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
2LA5_A	-	0.77	0.71	0.83	5	269	3	0	1	2	2
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	513	15	3	12	0	18
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
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2RPT_A	-	1.00	1.00	1.00	7	65	0	0	0	0	0
2RRC_A	-	1.00	1.00	1.00	7	68	0	0	0	0	0
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	13	0	0	13	0
2WW9_E	-	-0.03	0.00	0.00	0	168	5	0	4	1	5
2WW9_D	-	0.09	0.10	0.11	1	732	13	2	6	5	9
2WW9_F	-	0.52	0.63	0.50	5	102	5	1	4	0	3
2WWQ_V	tRNA links to Rfam database...	1.00	1.00	1.00	19	1185	5	0	0	5	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...	0.83	0.81	0.85	17	1109	4	0	3	1	4
2Y8W_B	-	1.00	1.00	1.00	6	82	1	0	0	1	0
2Y9C_V	-	0.79	0.83	0.75	15	886	8	0	5	3	3
2YIE_X	-	1.00	1.00	1.00	7	537	4	0	0	4	0
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
2ZY6_A	-	0.66	0.78	0.58	7	264	5	3	2	0	2
2ZZM_B	tRNA links to Rfam database...	0.29	0.33	0.26	5	1339	22	5	9	8	10
2ZZN_D	tRNA links to Rfam database...	0.52	0.55	0.52	12	961	11	3	8	0	10
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3ADB_C	-	0.98	0.97	1.00	32	1787	0	0	0	0	1
3AKZ_H	tRNA links to Rfam database...	0.43	0.45	0.43	9	1106	14	3	9	2	11
3AM1_B	-	1.00	1.00	1.00	29	1437	0	0	0	0	0
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3DW4_A	-	-0.03	0.00	0.00	0	136	6	1	3	2	6
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.53	0.54	0.54	15	1421	14	4	9	1	13
3HAY_E	-	1.00	1.00	1.00	14	910	4	0	0	4	0
3HJW_D	-	0.97	0.94	1.00	15	594	2	0	0	2	1
3IAB_R	-	1.00	1.00	1.00	12	373	0	0	0	0	0
3ID5_D	-	0.54	0.60	0.50	3	223	5	1	2	2	2
3IVN_B	Purine links to Rfam database...	0.88	0.78	1.00	18	885	0	0	0	0	5
3IWN_A	c-di-GMP-I links to Rfam database...	0.69	0.68	0.70	19	1445	9	1	7	1	9
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.35	0.36	0.36	4	400	8	3	4	1	7
3J0L_1	-	0.83	0.77	0.91	10	473	4	0	1	3	3
3J0L_7	-	-0.02	0.00	0.00	0	507	12	2	10	0	10
3J0L_g	-	-0.01	0.00	0.00	0	173	5	1	2	2	2
3J16_L	tRNA links to Rfam database...	0.49	0.52	0.48	11	1136	12	3	9	0	10
3J20_0	tRNA links to Rfam database...	0.51	0.57	0.48	12	1194	14	2	11	1	9
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1090	21	4	17	0	20
3KTW_C	-	1.00	1.00	1.00	25	1755	8	0	0	8	0
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.66	0.68	0.65	13	715	7	0	7	0	6
3NMU_E	-	1.00	1.00	1.00	3	213	5	0	0	5	0
3OVB_D	-	1.00	1.00	1.00	11	215	1	0	0	1	0
3OVS_D	-	1.00	1.00	1.00	12	204	0	0	0	0	0
3P22_G	-	1.00	1.00	1.00	11	301	0	0	0	0	0
3R4F_A	-	1.00	1.00	1.00	22	884	1	0	0	1	0
3R9X_C	-	1.00	1.00	1.00	8	221	2	0	0	2	0
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...	0.73	0.72	0.75	21	1505	7	4	3	0	8
3SIU_F	-	1.00	1.00	1.00	8	137	0	0	0	0	0
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
3W3S_B	tRNA-Sec links to Rfam database...	0.95	0.94	0.97	31	1957	2	0	1	1	2
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.62	0.62	0.64	18	1409	11	4	6	1	11
4ATO_G	-	0.36	0.43	0.33	3	211	6	6	0	0	4
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.36	0.33	0.42	5	484	7	0	7	0	10
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0

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Performance of RDfolder - scored lower in this pairwise comparison

1. Total counts & total scores for RDfolder

Total Base Pair Counts
Total TP	878
Total TN	53610
Total FP	383
Total FP CONTRA	75
Total FP INCONS	242
Total FP COMP	66
Total FN	500

Total Scores
MCC	0.677
Average MCC ± 95% Confidence Intervals	0.692 ± 0.073
Sensitivity	0.637
Positive Predictive Value	0.735
Nr of predictions	96

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2K5Z_A	-	0.79	0.64	1.00	7	179	0	0	0	0	4
2K63_A	-	0.94	0.89	1.00	8	160	0	0	0	0	1
2K66_A	-	0.94	0.89	1.00	8	81	0	0	0	0	1
2KD8_A	-	0.94	0.89	1.00	8	100	0	0	0	0	1
2KDQ_B	mir-TAR links to Rfam database...	1.00	1.00	1.00	10	164	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	0.91	0.83	1.00	15	452	1	0	0	1	3
2KEZ_A	-	1.00	1.00	1.00	8	94	0	0	0	0	0
2KFC_A	-	0.79	0.63	1.00	5	231	0	0	0	0	3
2KGP_A	-	1.00	1.00	1.00	9	112	0	0	0	0	0
2KMJ_A	-	1.00	1.00	1.00	11	157	0	0	0	0	0
2KPV_A	-	0.96	0.92	1.00	12	201	0	0	0	0	1
2KU0_A	-	-0.03	0.00	0.00	0	285	7	2	5	0	12
2KUR_A	K10_TLS links to Rfam database...	0.91	0.84	1.00	16	451	0	0	0	0	3
2KUU_A	K10_TLS links to Rfam database...	0.91	0.83	1.00	15	432	1	0	0	1	3
2KUV_A	K10_TLS links to Rfam database...	0.91	0.84	1.00	16	423	0	0	0	0	3
2KUW_A	K10_TLS links to Rfam database...	0.94	0.89	1.00	16	454	0	0	0	0	2
2KX8_A	7SK links to Rfam database...	0.93	0.88	1.00	14	357	0	0	0	0	2
2KXM_A	-	0.78	0.63	1.00	5	144	0	0	0	0	3
2KZL_A	-	1.00	1.00	1.00	13	507	4	0	0	4	0
2L1F_A	Gammaretro_CES links to Rfam database...	-0.02	0.00	0.00	0	750	13	2	11	0	23
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	0	0	0	0	0
2L2K_A	-	1.00	1.00	1.00	17	332	0	0	0	0	0
2L3C_B	-	1.00	1.00	1.00	14	225	0	0	0	0	0
2L3E_A	-	1.00	1.00	1.00	12	228	1	0	0	1	0
2L3J_B	mir-2985-2 links to Rfam database...	1.00	1.00	1.00	30	955	0	0	0	0	0
2L5Z_A	-	1.00	1.00	1.00	9	102	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
2LA5_A	-	0.77	0.71	0.83	5	269	1	0	1	0	2
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	514	14	3	11	0	18
2LDL_A	-	1.00	1.00	1.00	9	131	0	0	0	0	0
2LDT_A	-	0.79	0.64	1.00	7	155	0	0	0	0	4
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2RPT_A	-	-0.07	0.00	0.00	0	68	4	1	3	0	7
2RRC_A	-	0.83	0.71	1.00	5	70	0	0	0	0	2
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	13	0	0	13	0
2WW9_E	-	-0.03	0.00	0.00	0	168	5	0	4	1	5
2WW9_D	-	0.31	0.10	1.00	1	740	3	0	0	3	9
2WW9_F	-	0.86	0.75	1.00	6	106	1	0	0	1	2
2WWQ_V	tRNA links to Rfam database...	0.80	0.74	0.88	14	1188	4	0	2	2	5
2XKV_B	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	1813	22	10	12	0	11
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2Y8W_B	-	1.00	1.00	1.00	6	82	1	0	0	1	0
2Y9C_V	-	0.68	0.67	0.71	12	889	7	0	5	2	6
2YIE_X	-	0.57	0.57	0.57	4	537	5	0	3	2	3
2YIE_Z	-	0.53	0.63	0.45	5	591	6	4	2	0	3
2ZY6_A	-	0.66	0.78	0.58	7	264	5	3	2	0	2
2ZZM_B	tRNA links to Rfam database...	0.15	0.20	0.13	3	1334	21	7	14	0	12
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	2	2	0	0	1
3A2K_C	tRNA links to Rfam database...	0.98	0.95	1.00	21	1087	0	0	0	0	1
3A3A_A	tRNA-Sec links to Rfam database...	0.59	0.50	0.71	15	1479	6	0	6	0	15
3ADB_C	-	0.48	0.45	0.54	15	1791	13	1	12	0	18
3AKZ_H	tRNA links to Rfam database...	0.53	0.55	0.52	11	1106	12	1	9	2	9
3AM1_B	-	0.52	0.52	0.54	15	1438	13	4	9	0	14
3AMU_B	tRNA links to Rfam database...	0.20	0.21	0.22	4	1139	16	4	10	2	15
3DW4_A	-	-0.03	0.00	0.00	0	136	4	1	3	0	6
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.60	0.57	0.64	16	1424	10	2	7	1	12
3HAY_E	-	1.00	1.00	1.00	14	910	7	0	0	7	0
3HJW_D	-	0.90	0.88	0.93	14	594	3	0	1	2	2
3IAB_R	-	1.00	1.00	1.00	12	373	4	0	0	4	0
3ID5_D	-	-0.02	0.00	0.00	0	223	6	3	3	0	5
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	-0.01	0.00	0.00	0	1462	10	1	9	0	28
3J0L_8	-	0.92	0.86	1.00	6	70	0	0	0	0	1
3J0L_a	-	-0.02	0.00	0.00	0	407	4	3	1	0	11
3J0L_1	-	0.73	0.62	0.89	8	475	3	0	1	2	5
3J0L_7	-	-0.01	0.00	0.00	0	514	5	1	4	0	10
3J0L_g	-	-0.01	0.00	0.00	0	173	3	2	1	0	2
3J16_L	tRNA links to Rfam database...	0.26	0.24	0.31	5	1143	11	0	11	0	16
3J20_0	tRNA links to Rfam database...	0.82	0.76	0.89	16	1201	3	1	1	1	5
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1091	20	4	16	0	20
3KTW_C	-	0.11	0.12	0.13	3	1757	23	3	17	3	22
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.43	0.42	0.47	8	718	9	2	7	0	11
3NMU_E	-	0.57	0.33	1.00	1	215	3	0	0	3	2
3OVB_D	-	1.00	1.00	1.00	11	215	1	0	0	1	0
3OVS_D	-	1.00	1.00	1.00	12	204	0	0	0	0	0
3P22_G	-	0.95	0.91	1.00	10	302	0	0	0	0	1
3R4F_A	-	0.78	0.73	0.84	16	887	4	2	1	1	6
3R9X_C	-	1.00	1.00	1.00	8	221	2	0	0	2	0
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...	0.35	0.24	0.54	7	1520	6	1	5	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	0	0	0	0	0
3TS0_U	-	0.91	0.83	1.00	5	113	0	0	0	0	1
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.29	0.27	0.33	9	1962	18	2	16	0	24
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ATO_G	-	0.75	0.57	1.00	4	216	0	0	0	0	3
4ENB_A	crcB links to Rfam database...	0.48	0.40	0.60	6	462	4	0	4	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	0	4	0	9
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0

^top

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 RNAsubopt - scored higher in this pairwise comparison

1. Total counts & total scores for RNAsubopt

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

Performance of RDfolder - scored lower in this pairwise comparison

1. Total counts & total scores for RDfolder

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