CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	CentroidFold		Pknots
MCC	0.810	>	0.739
Average MCC ± 95% Confidence Intervals	0.809 ± 0.054	>	0.762 ± 0.062
Sensitivity	0.797	>	0.761
Positive Predictive Value	0.831	>	0.726
Total TP	1388	>	1325
Total TN	96353	>	96200
Total FP	464	<	690
Total FP CONTRA	82	<	157
Total FP INCONS	201	<	342
Total FP COMP	181	<	191
Total FN	353	<	416
P-value	3.56938820447e-08

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Performance plots

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

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Performance of CentroidFold - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidFold

Total Base Pair Counts
Total TP	1388
Total TN	96353
Total FP	464
Total FP CONTRA	82
Total FP INCONS	201
Total FP COMP	181
Total FN	353

Total Scores
MCC	0.810
Average MCC ± 95% Confidence Intervals	0.809 ± 0.054
Sensitivity	0.797
Positive Predictive Value	0.831
Nr of predictions	102

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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
2KD8_A	-	1.00	1.00	1.00	9	99	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	449	1	0	0	1	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
2KRL_A	-	0.91	0.87	0.95	20	2003	9	1	0	8	3
2KU0_A	-	0.53	0.42	0.71	5	285	2	2	0	0	7
2KUR_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	448	0	0	0	0	0
2KUU_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	429	1	0	0	1	0
2KUV_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	420	0	0	0	0	0
2KUW_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	452	1	0	0	1	0
2KX8_A	7SK links to Rfam database...	1.00	1.00	1.00	16	355	0	0	0	0	0
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...	1.00	1.00	1.00	23	740	0	0	0	0	0
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...	0.94	0.94	0.94	17	339	2	0	1	1	1
2LA5_A	-	0.77	0.71	0.83	5	269	2	0	1	1	2
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.51	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
2LWK_A	-	1.00	1.00	1.00	11	196	1	0	0	1	0
2RPT_A	-	1.00	1.00	1.00	7	65	0	0	0	0	0
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_D	-	0.31	0.10	1.00	1	740	3	0	0	3	9
2WW9_F	-	0.68	0.75	0.67	6	103	4	1	2	1	2
2WW9_E	-	0.00	0.00	0.00	0	172	0	0	0	0	5
2WWQ_V	tRNA links to Rfam database...	1.00	1.00	1.00	19	1185	3	0	0	3	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	27	0	6	21	3
2XQD_Y	tRNA links to Rfam database...	0.83	0.81	0.85	17	1109	4	0	3	1	4
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.13	0.11	0.17	4	2021	21	2	18	1	31
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_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
2ZZM_B	tRNA links to Rfam database...	0.13	0.13	0.15	2	1345	20	3	8	9	13
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	3	2	0	1	1
3A2K_C	tRNA links to Rfam database...	0.49	0.55	0.46	12	1082	14	3	11	0	10
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...	0.48	0.50	0.48	10	1106	13	3	8	2	10
3AM1_B	-	0.74	0.76	0.73	22	1436	8	3	5	0	7
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3GX2_A	SAM links to Rfam database...	0.94	0.89	1.00	25	1424	1	0	0	1	3
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...	0.86	0.79	0.96	22	1449	1	0	1	0	6
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	11	0	5	6	3
3J0L_2	-	0.28	0.31	0.28	8	2221	24	2	19	3	18
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_g	-	0.00	0.00	0.00	0	176	0	0	0	0	2
3J0L_7	-	-0.01	0.00	0.00	0	514	5	1	4	0	10
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J16_L	tRNA links to Rfam database...	0.59	0.57	0.63	12	1140	7	0	7	0	9
3JYV_7	tRNA links to Rfam database...	0.92	0.85	1.00	17	1094	2	0	0	2	3
3JYX_4	5_8S_rRNA links to Rfam database...	0.41	0.58	0.29	7	4732	25	11	6	8	5
3JYX_3	5S_rRNA links to Rfam database...	0.35	0.47	0.27	7	2352	21	14	5	2	8
3KTW_C	-	0.58	0.60	0.58	15	1754	18	1	10	7	10
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NDB_M	-	0.97	0.95	0.98	42	3671	6	0	1	5	2
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	3	0	0	3	0
3NPB_A	SAM links to Rfam database...	0.87	0.84	0.91	31	2244	8	1	2	5	6
3O58_2	5S_rRNA links to Rfam database...	0.95	0.94	0.97	29	2724	7	0	1	6	2
3O58_3	5_8S_rRNA links to Rfam database...	0.44	0.41	0.47	9	4745	11	1	9	1	13
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	1	0	0	1	0
3PDR_A	ykoK links to Rfam database...	0.88	0.86	0.90	43	4792	7	2	3	2	7
3R4F_A	-	0.83	0.82	0.86	18	885	4	2	1	1	4
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...	0.70	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
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
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

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Performance of Pknots - scored lower in this pairwise comparison

1. Total counts & total scores for Pknots

Total Base Pair Counts
Total TP	1325
Total TN	96200
Total FP	690
Total FP CONTRA	157
Total FP INCONS	342
Total FP COMP	191
Total FN	416

Total Scores
MCC	0.739
Average MCC ± 95% Confidence Intervals	0.762 ± 0.062
Sensitivity	0.761
Positive Predictive Value	0.726
Nr of predictions	102

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KD8_A	-	1.00	1.00	1.00	9	99	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	449	1	0	0	1	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
2KRL_A	-	0.79	0.83	0.76	19	1999	13	5	1	7	4
2KU0_A	-	-0.04	0.00	0.00	0	282	10	0	10	0	12
2KUR_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	448	0	0	0	0	0
2KUU_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	429	1	0	0	1	0
2KUV_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	420	0	0	0	0	0
2KUW_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	452	1	0	0	1	0
2KX8_A	7SK links to Rfam database...	1.00	1.00	1.00	16	355	0	0	0	0	0
2KXM_A	-	-0.04	0.00	0.00	0	144	5	0	5	0	8
2KZL_A	-	0.66	0.69	0.64	9	506	6	2	3	1	4
2L1F_A	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	23	740	0	0	0	0	0
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	-	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...	0.94	0.94	0.94	17	339	2	0	1	1	1
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...	0.83	0.83	0.83	15	510	3	2	1	0	3
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	-	0.48	0.55	0.43	16	2403	23	9	12	2	13
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	0.38	0.27	0.60	3	202	3	0	2	1	8
2RPT_A	-	1.00	1.00	1.00	7	65	0	0	0	0	0
2RRC_A	-	0.92	0.86	1.00	6	69	0	0	0	0	1
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	13	0	0	13	0
2WW9_D	-	0.52	0.60	0.46	6	728	13	5	2	6	4
2WW9_F	-	0.68	0.75	0.67	6	103	4	1	2	1	2
2WW9_E	-	0.79	0.80	0.80	4	167	3	0	1	2	1
2WWQ_V	tRNA links to Rfam database...	0.29	0.32	0.29	6	1183	16	3	12	1	13
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.21	0.27	0.17	3	1817	33	3	12	18	8
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.32	0.34	0.32	12	2008	26	1	24	1	23
2Y8W_B	-	1.00	1.00	1.00	6	82	1	0	0	1	0
2Y9C_V	-	0.70	0.67	0.75	12	890	6	0	4	2	6
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
2YIE_X	-	0.53	0.57	0.50	4	536	6	1	3	2	3
2ZZM_B	tRNA links to Rfam database...	0.18	0.20	0.19	3	1342	23	4	9	10	12
2ZZN_D	tRNA links to Rfam database...	0.95	0.95	0.95	21	962	1	1	0	0	1
3A2K_C	tRNA links to Rfam database...	0.50	0.55	0.48	12	1083	13	3	10	0	10
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...	1.00	1.00	1.00	20	1107	2	0	0	2	0
3AM1_B	-	1.00	1.00	1.00	29	1437	0	0	0	0	0
3AMU_B	tRNA links to Rfam database...	1.00	1.00	1.00	19	1138	3	0	0	3	0
3GX2_A	SAM links to Rfam database...	0.55	0.57	0.55	16	1420	14	4	9	1	12
3IAB_R	-	1.00	1.00	1.00	12	373	4	0	0	4	0
3ID5_D	-	-0.02	0.00	0.00	0	224	5	1	4	0	5
3IVN_B	Purine links to Rfam database...	0.91	0.87	0.95	20	882	1	0	1	0	3
3IWN_A	c-di-GMP-I links to Rfam database...	0.22	0.21	0.25	6	1448	18	2	16	0	22
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	9	0	5	4	3
3J0L_2	-	0.44	0.46	0.43	12	2222	23	1	15	7	14
3J0L_a	-	0.35	0.36	0.36	4	400	8	3	4	1	7
3J0L_1	-	0.73	0.62	0.89	8	475	3	0	1	2	5
3J0L_h	-	0.67	0.66	0.70	21	2110	11	4	5	2	11
3J0L_g	-	-0.02	0.00	0.00	0	171	5	3	2	0	2
3J0L_7	-	0.38	0.50	0.31	5	503	12	3	8	1	5
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J16_L	tRNA links to Rfam database...	0.41	0.43	0.41	9	1137	13	1	12	0	12
3JYV_7	tRNA links to Rfam database...	0.97	0.95	1.00	19	1092	2	0	0	2	1
3JYX_4	5_8S_rRNA links to Rfam database...	0.33	0.58	0.19	7	4720	41	22	7	12	5
3JYX_3	5S_rRNA links to Rfam database...	0.37	0.53	0.27	8	2348	26	17	5	4	7
3KTW_C	-	0.63	0.68	0.59	17	1751	18	3	9	6	8
3LA5_A	Purine links to Rfam database...	0.94	0.88	1.00	22	932	0	0	0	0	3
3NDB_M	-	0.92	0.93	0.91	41	3669	8	3	1	4	3
3NKB_B	-	0.64	0.68	0.62	13	714	8	0	8	0	6
3NMU_E	-	1.00	1.00	1.00	3	213	5	0	0	5	0
3NPB_A	SAM links to Rfam database...	0.84	0.81	0.88	30	2244	9	0	4	5	7
3O58_2	5S_rRNA links to Rfam database...	0.93	0.90	0.97	28	2725	3	0	1	2	3
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.45	0.24	10	4722	39	18	14	7	12
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
3PDR_A	ykoK links to Rfam database...	0.64	0.64	0.65	32	4791	19	4	13	2	18
3R4F_A	-	1.00	1.00	1.00	22	884	1	0	0	1	0
3R9X_C	-	0.87	0.88	0.88	7	221	5	0	1	4	1
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	0	1	0	3
3SD1_A	THF links to Rfam database...	0.78	0.76	0.81	22	1506	5	1	4	0	7
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	-	0.33	0.36	0.32	8	1251	17	4	13	0	14
3UZL_B	tRNA links to Rfam database...	1.00	1.00	1.00	16	1277	7	0	0	7	0
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
4A1C_3	5S_rRNA links to Rfam database...	0.28	0.30	0.28	11	2723	30	4	25	1	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.29	8	4488	36	9	11	16	12
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.19	0.21	0.21	6	1409	23	3	19	1	23
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	2	0	0	2	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	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 CentroidFold - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidFold

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

Performance of Pknots - scored lower in this pairwise comparison

1. Total counts & total scores for Pknots

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