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		RNAsubopt
MCC	0.780	>	0.737
Average MCC ± 95% Confidence Intervals	0.802 ± 0.054	>	0.772 ± 0.059
Sensitivity	0.775	>	0.758
Positive Predictive Value	0.791	>	0.724
Total TP	1462	>	1430
Total TN	144151	>	144025
Total FP	588	<	797
Total FP CONTRA	137	<	173
Total FP INCONS	250	<	372
Total FP COMP	201	<	252
Total FN	425	<	457
P-value	3.56938820447e-08

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Performance plots

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

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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	1462
Total TN	144151
Total FP	588
Total FP CONTRA	137
Total FP INCONS	250
Total FP COMP	201
Total FN	425

Total Scores
MCC	0.780
Average MCC ± 95% Confidence Intervals	0.802 ± 0.054
Sensitivity	0.775
Positive Predictive Value	0.791
Nr of predictions	104

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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_E	-	0.00	0.00	0.00	0	172	0	0	0	0	5
2WW9_F	-	0.68	0.75	0.67	6	103	4	1	2	1	2
2WW9_D	-	0.31	0.10	1.00	1	740	3	0	0	3	9
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_X	-	1.00	1.00	1.00	7	537	3	0	0	3	0
2YIE_Z	-	0.53	0.63	0.45	5	591	6	4	2	0	3
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
3IYQ_A	tmRNA links to Rfam database...	0.29	0.39	0.22	20	22347	86	39	34	13	31
3IZ4_A	tmRNA links to Rfam database...	0.60	0.57	0.64	54	25451	38	16	15	7	41
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	11	0	5	6	3
3J0L_a	-	0.41	0.36	0.50	4	403	5	3	1	1	7
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
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_g	-	0.00	0.00	0.00	0	176	0	0	0	0	2
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
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_3	5_8S_rRNA links to Rfam database...	0.44	0.41	0.47	9	4745	11	1	9	1	13
3O58_2	5S_rRNA links to Rfam database...	0.95	0.94	0.97	29	2724	7	0	1	6	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	-	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_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.19	5	4490	29	9	12	8	15
4A1C_3	5S_rRNA links to Rfam database...	0.80	0.78	0.83	29	2728	8	0	6	2	8
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 RNAsubopt - scored lower in this pairwise comparison

1. Total counts & total scores for RNAsubopt

Total Base Pair Counts
Total TP	1430
Total TN	144025
Total FP	797
Total FP CONTRA	173
Total FP INCONS	372
Total FP COMP	252
Total FN	457

Total Scores
MCC	0.737
Average MCC ± 95% Confidence Intervals	0.772 ± 0.059
Sensitivity	0.758
Positive Predictive Value	0.724
Nr of predictions	104

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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
2KD8_A	-	0.87	0.78	1.00	7	101	0	0	0	0	2
2KE6_A	K10_TLS links to Rfam database...	0.88	0.89	0.89	16	449	3	0	2	1	2
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	-	0.62	0.61	0.64	14	2002	15	5	3	7	9
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
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	-	0.85	0.86	0.83	25	2410	14	0	5	9	4
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	0.95	0.91	1.00	10	197	1	0	0	1	1
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_F	-	0.52	0.63	0.50	5	102	5	1	4	0	3
2WW9_D	-	0.09	0.10	0.11	1	732	13	2	6	5	9
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
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.49	0.49	0.52	17	2012	17	1	15	1	18
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
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
3GX2_A	SAM links to Rfam database...	0.53	0.54	0.54	15	1421	14	4	9	1	13
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
3IYQ_A	tmRNA links to Rfam database...	0.28	0.39	0.20	20	22342	96	41	37	18	31
3IZ4_A	tmRNA links to Rfam database...	0.56	0.60	0.53	57	25429	54	26	24	4	38
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	9	0	5	4	3
3J0L_a	-	0.35	0.36	0.36	4	400	8	3	4	1	7
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_1	-	0.83	0.77	0.91	10	473	4	0	1	3	3
3J0L_h	-	0.87	0.81	0.93	26	2112	4	1	1	2	6
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
3J0L_2	-	0.28	0.31	0.28	8	2221	25	2	19	4	18
3J16_L	tRNA links to Rfam database...	0.49	0.52	0.48	11	1136	12	3	9	0	10
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1090	21	4	17	0	20
3JYX_4	5_8S_rRNA links to Rfam database...	0.34	0.58	0.21	7	4722	38	20	7	11	5
3JYX_3	5S_rRNA links to Rfam database...	0.77	0.80	0.75	12	2362	26	0	4	22	3
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
3NDB_M	-	0.93	0.93	0.93	41	3670	9	0	3	6	3
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
3NPB_A	SAM links to Rfam database...	0.84	0.78	0.91	29	2246	8	0	3	5	8
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	35	6	15	14	11
3O58_2	5S_rRNA links to Rfam database...	0.87	0.90	0.85	28	2721	13	0	5	8	3
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...	0.90	0.90	0.90	45	4790	7	2	3	2	5
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
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3UZL_B	tRNA links to Rfam database...	0.49	0.50	0.50	8	1277	15	0	8	7	8
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4481	43	13	17	13	15
4A1C_3	5S_rRNA links to Rfam database...	0.85	0.84	0.86	31	2727	8	0	5	3	6
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
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

^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 RNAsubopt - scored lower in this pairwise comparison

1. Total counts & total scores for RNAsubopt

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