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	0.601	>	0.590
Average MCC ± 95% Confidence Intervals	0.659 ± 0.051	>	0.653 ± 0.051
Sensitivity	0.515	<	0.531
Positive Predictive Value	0.706	>	0.659
Total TP	1962	<	2023
Total TN	658342	>	658054
Total FP	933	<	1205
Total FP CONTRA	110	<	134
Total FP INCONS	708	<	911
Total FP COMP	115	<	160
Total FN	1845	>	1784
P-value	4.48494289621e-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	1962
Total TN	658342
Total FP	933
Total FP CONTRA	110
Total FP INCONS	708
Total FP COMP	115
Total FN	1845

Total Scores
MCC	0.601
Average MCC ± 95% Confidence Intervals	0.659 ± 0.051
Sensitivity	0.515
Positive Predictive Value	0.706
Nr of predictions	133

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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	222	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	0.97	0.95	1.00	18	1110	1	0	0	1	1
2KMJ_A	-	1.00	1.00	1.00	11	367	0	0	0	0	0
2KPV_A	-	0.96	0.92	1.00	12	549	0	0	0	0	1
2KRL_A	-	0.76	0.60	0.96	24	5126	5	0	1	4	16
2KU0_A	-	0.47	0.31	0.71	5	696	2	0	2	0	11
2KUR_A	K10_TLS links to Rfam database...	0.95	0.90	1.00	19	1109	0	0	0	0	2
2KUU_A	K10_TLS links to Rfam database...	0.92	0.86	1.00	18	1110	1	0	0	1	3
2KUV_A	K10_TLS links to Rfam database...	0.93	0.86	1.00	19	1109	0	0	0	0	3
2KUW_A	K10_TLS links to Rfam database...	0.95	0.90	1.00	19	1109	0	0	0	0	2
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2KXM_A	-	0.89	0.80	1.00	8	343	0	0	0	0	2
2KZL_A	-	0.86	0.74	1.00	14	1471	0	0	0	0	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L2K_A	-	0.94	0.89	1.00	17	844	0	0	0	0	2
2L3C_B	-	0.91	0.82	1.00	14	547	0	0	0	0	3
2L3E_A	-	0.96	0.92	1.00	12	583	1	0	0	1	1
2L3J_B	mir-2985-2 links to Rfam database...	0.94	0.88	1.00	30	2455	0	0	0	0	4
2L5Z_A	-	0.86	0.75	1.00	9	316	0	0	0	0	3
2L94_A	HIV_FE links to Rfam database...	0.92	0.90	0.95	18	971	1	0	1	0	2
2LA5_A	-	0.42	0.26	0.71	5	623	2	0	2	0	14
2LBS_A	-	1.00	1.00	1.00	14	482	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.49	0.35	0.70	7	1530	3	1	2	0	13
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LDT_A	-	0.85	0.73	1.00	11	454	0	0	0	0	4
2LHP_A	-	0.97	0.94	1.00	15	651	0	0	0	0	1
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LJJ_A	-	1.00	1.00	1.00	8	343	2	0	0	2	0
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.82	0.74	0.91	29	6073	4	0	3	1	10
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LU0_A	-	0.93	0.88	1.00	14	1162	0	0	0	0	2
2LWK_A	-	0.92	0.92	0.92	12	483	1	0	1	0	1
2M58_A	-	0.09	0.06	0.14	1	1646	6	0	6	0	16
2RPT_A	-	1.00	1.00	1.00	7	183	0	0	0	0	0
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	12	5	3	4	7
2WW9_D	-	0.29	0.12	0.75	3	1949	1	0	1	0	23
2WW9_E	-	0.00	0.00	0.00	0	561	0	0	0	0	14
2WW9_F	-	0.59	0.60	0.60	6	290	4	0	4	0	4
2WWQ_V	tRNA links to Rfam database...	0.80	0.68	0.95	19	2906	3	0	1	2	9
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.51	0.50	0.53	10	4541	25	0	9	16	10
2XQD_Y	tRNA links to Rfam database...	0.75	0.67	0.86	18	2829	3	0	3	0	9
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.15	0.12	0.20	5	5126	20	1	19	0	37
2Y8W_B	-	1.00	1.00	1.00	6	184	1	0	0	1	0
2Y9C_V	-	0.66	0.63	0.71	15	2257	8	1	5	2	9
2YIE_Z	-	0.43	0.42	0.45	5	1529	6	3	3	0	7
2YIE_X	-	0.67	0.58	0.78	7	1369	3	1	1	1	5
2ZZM_B	tRNA links to Rfam database...	0.18	0.16	0.23	5	3464	17	3	14	0	27
2ZZN_D	tRNA links to Rfam database...	0.82	0.78	0.88	21	2461	3	0	3	0	6
3A2K_C	tRNA links to Rfam database...	0.44	0.43	0.46	12	2900	14	2	12	0	16
3A3A_A	tRNA-Sec links to Rfam database...	0.87	0.76	1.00	28	3627	0	0	0	0	9
3ADB_C	-	0.92	0.84	1.00	32	4154	0	0	0	0	6
3AKZ_H	tRNA links to Rfam database...	0.43	0.39	0.48	11	2678	12	2	10	0	17
3AM1_B	-	0.68	0.63	0.73	22	3210	8	1	7	0	13
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3GX2_A	SAM links to Rfam database...	0.79	0.63	1.00	25	4346	1	0	0	1	15
3IAB_R	-	0.86	0.86	0.86	12	1021	4	1	1	2	2
3ID5_D	-	-0.01	0.00	0.00	0	490	6	3	3	0	9
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IWN_A	c-di-GMP-I links to Rfam database...	0.80	0.67	0.96	22	4255	1	0	1	0	11
3IYQ_A	tmRNA links to Rfam database...	0.36	0.37	0.34	35	60624	71	17	50	4	59
3IZ4_A	tmRNA links to Rfam database...	0.55	0.45	0.68	59	70789	33	4	24	5	73
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.61	0.77	33	6860	10	1	9	0	21
3J0L_2	-	0.25	0.24	0.28	8	6187	24	0	21	3	25
3J0L_g	-	0.00	0.00	0.00	0	465	0	0	0	0	4
3J0L_7	-	-0.01	0.00	0.00	0	1220	5	0	5	0	17
3J0L_h	-	0.77	0.65	0.90	28	6074	5	0	3	2	15
3J0L_1	-	0.65	0.47	0.90	9	1215	2	0	1	1	10
3J0L_a	-	0.41	0.31	0.56	5	1119	4	2	2	0	11
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J16_L	tRNA links to Rfam database...	0.50	0.40	0.63	12	2756	7	0	7	0	18
3J20_1	tRNA links to Rfam database...	0.91	0.87	0.95	20	2905	2	0	1	1	3
3J20_0	tRNA links to Rfam database...	0.44	0.40	0.50	12	2826	13	0	12	1	18
3J2C_M	-	0.40	0.29	0.57	59	106387	47	5	40	2	148
3J2C_O	-	0.76	0.65	0.89	41	10250	6	0	5	1	22
3J2L_3	5S_rRNA links to Rfam database...	0.53	0.49	0.58	26	7830	21	0	19	2	27
3J3D_C	tRNA links to Rfam database...	0.49	0.43	0.57	12	2754	9	0	9	0	16
3J3E_7	5S_rRNA links to Rfam database...	0.46	0.37	0.59	20	7106	14	1	13	0	34
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7485	21	2	16	3	33
3J3F_7	5S_rRNA links to Rfam database...	0.20	0.18	0.23	9	7221	30	1	29	0	41
3J3F_8	5_8S_rRNA links to Rfam database...	0.34	0.33	0.34	12	12211	34	4	19	11	24
3J3V_B	5S_rRNA links to Rfam database...	0.47	0.37	0.60	21	6986	14	1	13	0	36
3JYV_7	tRNA links to Rfam database...	0.77	0.59	1.00	19	2831	0	0	0	0	13
3JYX_4	5_8S_rRNA links to Rfam database...	0.23	0.21	0.25	7	12218	25	5	16	4	26
3JYX_3	5S_rRNA links to Rfam database...	0.29	0.30	0.30	8	6301	20	8	11	1	19
3KTW_C	-	0.45	0.40	0.53	17	4528	16	2	13	1	26
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NDB_M	-	0.80	0.70	0.91	43	9133	5	0	4	1	18
3NKB_B	-	0.57	0.50	0.65	13	1996	7	0	7	0	13
3NMU_E	-	0.71	0.50	1.00	3	558	3	0	0	3	3
3NPB_A	SAM links to Rfam database...	0.77	0.70	0.86	32	6984	7	1	4	2	14
3O58_2	5S_rRNA links to Rfam database...	0.82	0.76	0.88	29	7227	7	1	3	3	9
3O58_3	5_8S_rRNA links to Rfam database...	0.38	0.29	0.50	10	12383	10	0	10	0	25
3OVB_D	-	1.00	1.00	1.00	11	584	1	0	0	1	0
3OVS_D	-	0.96	0.92	1.00	12	549	0	0	0	0	1
3P22_G	-	0.96	0.92	1.00	11	730	1	0	0	1	1
3PDR_A	ykoK links to Rfam database...	0.73	0.60	0.90	43	12832	7	0	5	2	29
3R4F_A	-	0.81	0.76	0.86	19	2123	3	1	2	0	6
3R9X_C	-	0.84	0.80	0.89	8	586	2	0	1	1	2
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.58	0.48	0.71	20	3888	8	1	7	0	22
3SIU_F	-	0.79	0.64	1.00	7	371	0	0	0	0	4
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3TRZ_Z	-	0.91	0.83	1.00	5	205	1	0	0	1	1
3TS0_U	-	1.00	1.00	1.00	6	247	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3U4M_B	-	0.57	0.46	0.71	17	3136	7	0	7	0	20
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W1K_J	tRNA-Sec links to Rfam database...	0.56	0.50	0.63	19	4156	11	2	9	0	19
3W3S_B	tRNA-Sec links to Rfam database...	0.87	0.78	0.97	31	4721	2	0	1	1	9
3ZEX_C	5_8S_rRNA links to Rfam database...	0.47	0.27	0.82	14	14179	3	1	2	0	38
3ZEX_G	-	0.36	0.28	0.46	21	16425	29	2	23	4	53
3ZEX_F	-	0.00	0.00	0.00	0	2619	9	2	7	0	12
3ZEX_E	-	0.00	0.00	0.00	0	21895	52	3	47	2	77
3ZEX_H	-	0.19	0.18	0.21	7	9011	27	4	23	0	31
3ZEX_D	5S_rRNA links to Rfam database...	0.73	0.59	0.91	29	6989	3	0	3	0	20
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	23	1	20	2	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11752	29	5	19	5	28
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.56	0.81	30	7103	7	1	6	0	24
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.45	0.33	0.61	14	4348	10	1	8	1	28
4ATO_G	-	0.31	0.20	0.50	2	524	2	0	2	0	8
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.73	0.58	0.92	11	1314	1	1	0	0	8
4FNJ_A	-	0.15	0.13	0.22	2	586	7	0	7	0	14
4FRG_B	AdoCbl-variant links to Rfam database...	0.24	0.22	0.28	7	3461	18	3	15	0	25
4FRN_A	AdoCbl-variant links to Rfam database...	0.40	0.28	0.59	10	5134	7	2	5	0	26
4HXH_A	-	1.00	1.00	1.00	6	319	0	0	0	0	0
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12
4JRC_A	-	0.81	0.70	0.94	16	1523	1	0	1	0	7

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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	2023
Total TN	658054
Total FP	1205
Total FP CONTRA	134
Total FP INCONS	911
Total FP COMP	160
Total FN	1784

Total Scores
MCC	0.590
Average MCC ± 95% Confidence Intervals	0.653 ± 0.051
Sensitivity	0.531
Positive Predictive Value	0.659
Nr of predictions	133

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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	-	0.88	0.78	1.00	7	224	0	0	0	0	2
2KE6_A	K10_TLS links to Rfam database...	0.86	0.84	0.89	16	1110	3	0	2	1	3
2KMJ_A	-	1.00	1.00	1.00	11	367	0	0	0	0	0
2KPV_A	-	0.96	0.92	1.00	12	549	0	0	0	0	1
2KRL_A	-	0.52	0.43	0.65	17	5125	12	3	6	3	23
2KU0_A	-	0.83	0.69	1.00	11	692	0	0	0	0	5
2KUR_A	K10_TLS links to Rfam database...	0.85	0.81	0.89	17	1109	2	0	2	0	4
2KUU_A	K10_TLS links to Rfam database...	0.82	0.76	0.89	16	1110	3	0	2	1	5
2KUV_A	K10_TLS links to Rfam database...	0.83	0.77	0.89	17	1109	2	0	2	0	5
2KUW_A	K10_TLS links to Rfam database...	0.90	0.86	0.95	18	1109	1	0	1	0	3
2KX8_A	7SK links to Rfam database...	0.91	0.83	1.00	15	846	0	0	0	0	3
2KXM_A	-	0.89	0.80	1.00	8	343	0	0	0	0	2
2KZL_A	-	0.86	0.74	1.00	14	1471	0	0	0	0	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.94	0.88	1.00	22	2123	0	0	0	0	3
2L1F_A	Gammaretro_CES links to Rfam database...	0.93	0.88	1.00	21	2059	0	0	0	0	3
2L2K_A	-	0.94	0.89	1.00	17	844	0	0	0	0	2
2L3C_B	-	0.87	0.76	1.00	13	548	0	0	0	0	4
2L3E_A	-	0.96	0.92	1.00	12	583	1	0	0	1	1
2L3J_B	mir-2985-2 links to Rfam database...	0.94	0.88	1.00	30	2455	0	0	0	0	4
2L5Z_A	-	0.86	0.75	1.00	9	316	0	0	0	0	3
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LA5_A	-	0.39	0.26	0.63	5	622	3	1	2	0	14
2LBS_A	-	1.00	1.00	1.00	14	482	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LDT_A	-	0.85	0.73	1.00	11	454	0	0	0	0	4
2LHP_A	-	0.97	0.94	1.00	15	651	0	0	0	0	1
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LJJ_A	-	1.00	1.00	1.00	8	343	2	0	0	2	0
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.81	0.77	0.86	30	6070	9	0	5	4	9
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LU0_A	-	1.00	1.00	1.00	16	1160	0	0	0	0	0
2LWK_A	-	0.83	0.77	0.91	10	485	1	0	1	0	3
2M58_A	-	0.51	0.41	0.64	7	1642	4	1	3	0	10
2RPT_A	-	1.00	1.00	1.00	7	183	0	0	0	0	0
2RRC_A	-	0.83	0.70	1.00	7	224	0	0	0	0	3
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	12	5	3	4	7
2WW9_D	-	0.15	0.12	0.21	3	1939	11	4	7	0	23
2WW9_E	-	-0.01	0.00	0.00	0	556	5	0	5	0	14
2WW9_F	-	0.59	0.60	0.60	6	290	4	0	4	0	4
2WWQ_V	tRNA links to Rfam database...	0.76	0.68	0.86	19	2904	5	0	3	2	9
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.51	0.50	0.53	10	4541	23	0	9	14	10
2XQD_Y	tRNA links to Rfam database...	0.75	0.67	0.86	18	2829	3	0	3	0	9
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.47	0.43	0.53	18	5117	16	1	15	0	24
2Y8W_B	-	1.00	1.00	1.00	6	184	1	0	0	1	0
2Y9C_V	-	0.66	0.63	0.71	15	2257	8	1	5	2	9
2YIE_Z	-	-0.01	0.00	0.00	0	1525	15	3	12	0	12
2YIE_X	-	0.82	0.67	1.00	8	1370	3	0	0	3	4
2ZZM_B	tRNA links to Rfam database...	0.23	0.22	0.26	7	3459	20	2	18	0	25
2ZZN_D	tRNA links to Rfam database...	0.48	0.44	0.52	12	2462	11	1	10	0	15
3A2K_C	tRNA links to Rfam database...	0.42	0.39	0.46	11	2902	13	2	11	0	17
3A3A_A	tRNA-Sec links to Rfam database...	0.87	0.76	1.00	28	3627	0	0	0	0	9
3ADB_C	-	0.92	0.84	1.00	32	4154	0	0	0	0	6
3AKZ_H	tRNA links to Rfam database...	0.39	0.36	0.43	10	2678	13	2	11	0	18
3AM1_B	-	0.91	0.83	1.00	29	3211	0	0	0	0	6
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3GX2_A	SAM links to Rfam database...	0.44	0.38	0.54	15	4343	14	1	12	1	25
3IAB_R	-	0.92	0.86	1.00	12	1023	0	0	0	0	2
3ID5_D	-	0.40	0.33	0.50	3	490	5	0	3	2	6
3IVN_B	Purine links to Rfam database...	0.76	0.58	1.00	18	2328	0	0	0	0	13
3IWN_A	c-di-GMP-I links to Rfam database...	0.63	0.58	0.70	19	4251	9	0	8	1	14
3IYQ_A	tmRNA links to Rfam database...	0.33	0.36	0.30	34	60614	82	17	61	4	60
3IZ4_A	tmRNA links to Rfam database...	0.51	0.47	0.56	62	70766	49	8	40	1	70
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.61	0.80	33	6862	8	1	7	0	21
3J0L_2	-	0.25	0.24	0.28	8	6187	25	0	21	4	25
3J0L_g	-	-0.01	0.00	0.00	0	460	5	1	4	0	4
3J0L_7	-	-0.01	0.00	0.00	0	1213	12	0	12	0	17
3J0L_h	-	0.75	0.60	0.93	26	6077	4	0	2	2	17
3J0L_1	-	0.76	0.63	0.92	12	1212	2	0	1	1	7
3J0L_a	-	0.35	0.31	0.42	5	1116	7	1	6	0	11
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J16_L	tRNA links to Rfam database...	0.41	0.37	0.48	11	2752	12	1	11	0	19
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	2	0	0	2	2
3J20_0	tRNA links to Rfam database...	0.43	0.40	0.48	12	2825	14	0	13	1	18
3J2C_M	-	0.44	0.37	0.52	76	106346	72	8	61	3	131
3J2C_O	-	0.56	0.49	0.65	31	10248	17	1	16	0	32
3J2L_3	5S_rRNA links to Rfam database...	0.61	0.53	0.72	28	7836	13	0	11	2	25
3J3D_C	tRNA links to Rfam database...	0.61	0.57	0.67	16	2751	8	0	8	0	12
3J3E_7	5S_rRNA links to Rfam database...	0.59	0.50	0.69	27	7101	12	1	11	0	27
3J3E_8	5_8S_rRNA links to Rfam database...	0.16	0.15	0.18	5	7475	32	2	21	9	28
3J3F_7	5S_rRNA links to Rfam database...	0.80	0.70	0.92	35	7222	4	0	3	1	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.33	0.32	12	12209	39	4	21	14	24
3J3V_B	5S_rRNA links to Rfam database...	0.54	0.42	0.71	24	6987	10	1	9	0	33
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2829	21	0	21	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.19	0.21	0.17	7	12204	38	11	24	3	26
3JYX_3	5S_rRNA links to Rfam database...	0.63	0.63	0.63	17	6301	21	1	9	11	10
3KTW_C	-	0.75	0.65	0.88	28	4528	5	2	2	1	15
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NDB_M	-	0.77	0.69	0.86	42	9131	8	0	7	1	19
3NKB_B	-	0.57	0.50	0.65	13	1996	7	0	7	0	13
3NMU_E	-	0.54	0.50	0.60	3	556	5	0	2	3	3
3NPB_A	SAM links to Rfam database...	0.75	0.65	0.86	30	6986	7	1	4	2	16
3O58_2	5S_rRNA links to Rfam database...	0.72	0.74	0.70	28	7220	13	4	8	1	10
3O58_3	5_8S_rRNA links to Rfam database...	0.34	0.34	0.34	12	12368	34	2	21	11	23
3OVB_D	-	1.00	1.00	1.00	11	584	1	0	0	1	0
3OVS_D	-	0.96	0.92	1.00	12	549	0	0	0	0	1
3P22_G	-	0.96	0.92	1.00	11	730	0	0	0	0	1
3PDR_A	ykoK links to Rfam database...	0.75	0.63	0.90	45	12830	7	1	4	2	27
3R4F_A	-	0.96	0.92	1.00	23	2122	0	0	0	0	2
3R9X_C	-	0.84	0.80	0.89	8	586	2	0	1	1	2
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.61	0.50	0.75	21	3888	7	1	6	0	21
3SIU_F	-	0.85	0.73	1.00	8	370	0	0	0	0	3
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3TRZ_Z	-	0.91	0.83	1.00	5	205	1	0	0	1	1
3TS0_U	-	1.00	1.00	1.00	6	247	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.48	0.38	0.61	14	3547	9	0	9	0	23
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W1K_J	tRNA-Sec links to Rfam database...	0.87	0.79	0.97	30	4155	1	1	0	0	8
3W3S_B	tRNA-Sec links to Rfam database...	0.87	0.78	0.97	31	4721	2	0	1	1	9
3ZEX_C	5_8S_rRNA links to Rfam database...	0.24	0.21	0.28	11	14157	42	1	27	14	41
3ZEX_G	-	0.46	0.42	0.52	31	16411	32	3	26	3	43
3ZEX_F	-	0.00	0.00	0.00	0	2617	11	2	9	0	12
3ZEX_E	-	0.00	0.00	0.00	0	21893	54	4	48	2	77
3ZEX_H	-	0.18	0.18	0.18	7	9006	32	6	26	0	31
3ZEX_D	5S_rRNA links to Rfam database...	0.80	0.69	0.92	34	6984	3	0	3	0	15
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	23	1	20	2	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.13	5	11742	43	5	29	9	28
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.52	0.43	0.64	18	4343	11	2	8	1	24
4ATO_G	-	0.30	0.30	0.33	3	519	6	2	4	0	7
4ENB_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1262	2	1	1	0	8
4ENC_A	crcB links to Rfam database...	0.32	0.26	0.42	5	1314	7	0	7	0	14
4FNJ_A	-	0.79	0.63	1.00	10	585	0	0	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.32	0.28	0.38	9	3462	15	0	15	0	23
4FRN_A	AdoCbl-variant links to Rfam database...	0.51	0.44	0.59	16	5124	11	3	8	0	20
4HXH_A	-	1.00	1.00	1.00	6	319	0	0	0	0	0
4JF2_A	preQ1-II links to Rfam database...	0.61	0.52	0.73	16	2828	6	3	3	0	15
4JRC_A	-	0.29	0.26	0.35	6	1523	11	0	11	0	17

^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 ]