CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Contrafold		RNAshapes
MCC	0.618	>	0.602
Average MCC ± 95% Confidence Intervals	0.692 ± 0.048	>	0.675 ± 0.050
Sensitivity	0.550	>	0.533
Positive Predictive Value	0.700	>	0.685
Total TP	1993	>	1934
Total TN	615823	<	615845
Total FP	988	<	1035
Total FP CONTRA	124	>	104
Total FP INCONS	729	<	786
Total FP COMP	135	<	145
Total FN	1633	<	1692
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of Contrafold and RNAshapes. 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 Contrafold and RNAshapes).
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 Contrafold and RNAshapes).
Comparison of average Matthews Correlation Coefficients (MCCs) for Contrafold and RNAshapes. 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 Contrafold and RNAshapes).

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Performance of Contrafold - scored higher in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP	1993
Total TN	615823
Total FP	988
Total FP CONTRA	124
Total FP INCONS	729
Total FP COMP	135
Total FN	1633

Total Scores
MCC	0.618
Average MCC ± 95% Confidence Intervals	0.692 ± 0.048
Sensitivity	0.550
Positive Predictive Value	0.700
Nr of predictions	135

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2K5Z_A	-	1.00	1.00	1.00	11	395	0	0	0	0	0
2K63_A	-	0.90	0.90	0.90	9	396	2	0	1	1	1
2K66_A	-	0.95	0.90	1.00	9	222	0	0	0	0	1
2KD8_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2KE6_A	K10_TLS links to Rfam database...	0.97	0.95	1.00	18	1110	1	0	0	1	1
2KEZ_A	-	0.89	0.80	1.00	8	268	0	0	0	0	2
2KFC_A	-	0.45	0.25	0.83	5	624	1	0	1	0	15
2KGP_A	-	1.00	1.00	1.00	9	291	1	0	0	1	0
2KMJ_A	-	1.00	1.00	1.00	11	367	0	0	0	0	0
2KPV_A	-	1.00	1.00	1.00	13	548	0	0	0	0	0
2KRL_A	-	0.76	0.60	0.96	24	5126	5	0	1	4	16
2KU0_A	-	0.55	0.44	0.70	7	693	3	0	3	0	9
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	-	0.75	0.74	0.78	14	1467	4	2	2	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	-	0.39	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...	0.45	0.35	0.58	7	1528	5	2	3	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	-	0.84	0.79	0.89	31	6070	6	0	4	2	8
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LWK_A	-	0.88	0.85	0.92	11	484	1	0	1	0	2
2RP0_A	-	0.64	0.42	1.00	5	346	0	0	0	0	7
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	13	5	3	5	7
2WW9_E	-	0.00	0.00	0.00	0	561	0	0	0	0	14
2WW9_D	-	0.39	0.23	0.67	6	1944	3	2	1	0	20
2WW9_F	-	0.59	0.60	0.60	6	290	4	0	4	0	4
2WWQ_V	tRNA links to Rfam database...	0.78	0.68	0.90	19	2905	4	0	2	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...	0.78	0.70	0.86	19	2828	3	0	3	0	8
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.13	0.12	0.15	5	5117	29	1	28	0	37
2Y8W_B	-	1.00	1.00	1.00	6	184	3	0	0	3	0
2Y9C_V	-	0.66	0.63	0.71	15	2257	8	1	5	2	9
2YIE_X	-	0.73	0.67	0.80	8	1368	3	1	1	1	4
2YIE_Z	-	0.43	0.42	0.45	5	1529	6	3	3	0	7
2ZY6_A	-	0.58	0.58	0.58	7	691	5	0	5	0	5
2ZZM_B	tRNA links to Rfam database...	0.53	0.47	0.60	15	3461	10	2	8	0	17
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...	0.39	0.39	0.41	11	2674	17	4	12	1	17
3AM1_B	-	0.68	0.63	0.73	22	3210	8	1	7	0	13
3AMU_B	tRNA links to Rfam database...	0.65	0.59	0.73	16	2981	8	0	6	2	11
3DW4_A	-	-0.02	0.00	0.00	0	345	6	0	6	0	10
3G4S_9	5S_rRNA links to Rfam database...	0.30	0.25	0.38	14	7344	23	1	22	0	43
3GCA_A	-	0.49	0.29	0.83	5	522	1	0	1	0	12
3GX2_A	SAM links to Rfam database...	0.77	0.63	0.96	25	4345	2	0	1	1	15
3HAY_E	-	0.91	0.83	1.00	15	2263	6	0	0	6	3
3HJW_D	-	0.94	0.89	1.00	16	1637	2	0	0	2	2
3IAB_R	-	0.86	0.86	0.86	12	1021	4	1	1	2	2
3ID5_D	-	0.49	0.33	0.75	3	492	6	0	1	5	6
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...	0.34	0.37	0.32	35	60615	80	21	55	4	59
3IZ4_A	tmRNA links to Rfam database...	0.52	0.45	0.61	60	70777	44	4	35	5	72
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.61	0.77	33	6860	10	1	9	0	21
3J0L_g	-	0.00	0.00	0.00	0	464	1	1	0	0	4
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_a	-	0.50	0.44	0.58	7	1116	5	2	3	0	9
3J0L_1	-	0.73	0.58	0.92	11	1213	2	0	1	1	8
3J0L_h	-	0.75	0.65	0.88	28	6073	6	0	4	2	15
3J0L_7	-	-0.01	0.00	0.00	0	1218	7	0	7	0	17
3J0L_2	-	0.25	0.24	0.28	8	6187	26	0	21	5	25
3J16_L	tRNA links to Rfam database...	0.46	0.40	0.55	12	2753	10	1	9	0	18
3J20_0	tRNA links to Rfam database...	0.44	0.40	0.50	12	2826	13	0	12	1	18
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	4	0	0	4	2
3J2C_O	-	0.79	0.67	0.93	42	10251	4	0	3	1	21
3J2C_M	-	0.43	0.34	0.53	71	106357	66	9	54	3	136
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.49	0.65	26	7835	16	0	14	2	27
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2830	20	0	20	0	32
3JYX_3	5S_rRNA links to Rfam database...	0.28	0.30	0.27	8	6298	23	8	14	1	19
3JYX_4	5_8S_rRNA links to Rfam database...	0.20	0.21	0.20	7	12211	35	6	22	7	26
3KTW_C	-	0.44	0.40	0.50	17	4526	18	2	15	1	26
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NDB_M	-	0.81	0.72	0.92	44	9132	5	0	4	1	17
3NKB_B	-	0.54	0.50	0.59	13	1994	9	0	9	0	13
3NMU_E	-	0.71	0.50	1.00	3	558	3	0	0	3	3
3NPB_A	SAM links to Rfam database...	0.76	0.70	0.84	32	6983	8	1	5	2	14
3O58_2	5S_rRNA links to Rfam database...	0.78	0.76	0.81	29	7224	10	2	5	3	9
3O58_3	5_8S_rRNA links to Rfam database...	0.28	0.26	0.31	9	12374	20	3	17	0	26
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...	0.69	0.60	0.80	43	12826	13	0	11	2	29
3R4F_A	-	0.79	0.76	0.83	19	2122	4	1	3	0	6
3R9X_C	-	0.84	0.80	0.89	8	586	2	0	1	1	2
3RKF_A	Purine links to Rfam database...	0.73	0.59	0.91	20	2189	2	1	1	0	14
3SD1_A	THF links to Rfam database...	0.57	0.48	0.69	20	3887	9	2	7	0	22
3SIU_F	-	0.74	0.64	0.88	7	370	1	0	1	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	-	0.59	0.46	0.77	17	3138	5	0	5	0	20
3UZL_B	tRNA links to Rfam database...	0.70	0.54	0.91	20	3548	2	0	2	0	17
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.89	0.80	1.00	32	4721	1	0	0	1	8
3ZEX_G	-	0.28	0.24	0.33	18	16416	41	2	35	4	56
3ZEX_H	-	0.17	0.18	0.17	7	9003	35	6	29	0	31
3ZEX_D	5S_rRNA links to Rfam database...	0.73	0.67	0.80	33	6980	8	1	7	0	16
3ZEX_F	-	0.00	0.00	0.00	0	2619	9	2	7	0	12
3ZEX_E	-	0.00	0.00	0.00	0	21889	58	4	52	2	77
3ZEX_C	5_8S_rRNA links to Rfam database...	0.28	0.21	0.38	11	14167	22	3	15	4	41
4A1C_3	5S_rRNA links to Rfam database...	0.66	0.57	0.78	31	7100	9	1	8	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11751	33	5	20	8	28
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.44	0.36	0.56	15	4344	13	1	11	1	27
4ATO_G	-	0.44	0.40	0.50	4	520	4	0	4	0	6
4ENB_A	crcB links to Rfam database...	0.73	0.58	0.92	11	1263	1	1	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	-	0.79	0.63	1.00	10	585	0	0	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.68	0.56	0.82	18	3464	4	1	3	0	14
4FRN_A	AdoCbl-variant links to Rfam database...	0.65	0.56	0.77	20	5125	6	1	5	0	16
4HXH_A	-	1.00	1.00	1.00	6	319	0	0	0	0	0

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Performance of RNAshapes - scored lower in this pairwise comparison

1. Total counts & total scores for RNAshapes

Total Base Pair Counts
Total TP	1934
Total TN	615845
Total FP	1035
Total FP CONTRA	104
Total FP INCONS	786
Total FP COMP	145
Total FN	1692

Total Scores
MCC	0.602
Average MCC ± 95% Confidence Intervals	0.675 ± 0.050
Sensitivity	0.533
Positive Predictive Value	0.685
Nr of predictions	135

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2K5Z_A	-	1.00	1.00	1.00	11	395	0	0	0	0	0
2K63_A	-	0.95	0.90	1.00	9	397	0	0	0	0	1
2K66_A	-	0.95	0.90	1.00	9	222	0	0	0	0	1
2KD8_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2KE6_A	K10_TLS links to Rfam database...	0.97	0.95	1.00	18	1110	1	0	0	1	1
2KEZ_A	-	0.89	0.80	1.00	8	268	0	0	0	0	2
2KFC_A	-	-0.02	0.00	0.00	0	623	7	0	7	0	20
2KGP_A	-	1.00	1.00	1.00	9	291	1	0	0	1	0
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	-	0.83	0.69	1.00	11	692	0	0	0	0	5
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...	0.91	0.83	1.00	15	846	0	0	0	0	3
2KXM_A	-	0.83	0.70	1.00	7	344	0	0	0	0	3
2KZL_A	-	0.86	0.74	1.00	14	1471	0	0	0	0	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.96	0.92	1.00	23	2122	0	0	0	0	2
2L1F_A	Gammaretro_CES links to Rfam database...	0.87	0.83	0.91	20	2058	2	0	2	0	4
2L2K_A	-	0.92	0.84	1.00	16	845	0	0	0	0	3
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...	0.92	0.85	1.00	29	2456	0	0	0	0	5
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...	0.61	0.55	0.69	11	1524	5	0	5	0	9
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	-	0.93	0.87	1.00	34	6071	1	0	0	1	5
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LWK_A	-	0.83	0.77	0.91	10	485	1	0	1	0	3
2RP0_A	-	0.64	0.42	1.00	5	346	0	0	0	0	7
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...	0.59	0.59	0.59	10	2833	12	4	3	5	7
2WW9_E	-	0.53	0.29	1.00	4	557	0	0	0	0	10
2WW9_D	-	0.16	0.12	0.25	3	1941	9	4	5	0	23
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	22	0	9	13	10
2XQD_Y	tRNA links to Rfam database...	0.64	0.56	0.75	15	2830	5	0	5	0	12
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.93	0.86	1.00	36	5115	0	0	0	0	6
2Y8W_B	-	1.00	1.00	1.00	6	184	1	0	0	1	0
2Y9C_V	-	0.65	0.63	0.68	15	2256	8	1	6	1	9
2YIE_X	-	0.25	0.25	0.27	3	1367	11	1	7	3	9
2YIE_Z	-	-0.01	0.00	0.00	0	1525	15	3	12	0	12
2ZY6_A	-	0.58	0.58	0.58	7	691	5	0	5	0	5
2ZZM_B	tRNA links to Rfam database...	0.10	0.09	0.12	3	3460	23	0	23	0	29
2ZZN_D	tRNA links to Rfam database...	0.69	0.63	0.77	17	2463	5	1	4	0	10
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...	0.76	0.65	0.89	24	3628	3	0	3	0	13
3ADB_C	-	0.67	0.61	0.74	23	4155	8	0	8	0	15
3AKZ_H	tRNA links to Rfam database...	0.68	0.61	0.77	17	2679	6	1	4	1	11
3AM1_B	-	0.64	0.60	0.70	21	3210	9	1	8	0	14
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3DW4_A	-	-0.02	0.00	0.00	0	348	3	0	3	0	10
3G4S_9	5S_rRNA links to Rfam database...	0.41	0.32	0.53	18	7347	16	1	15	0	39
3GCA_A	-	0.54	0.29	1.00	5	523	0	0	0	0	12
3GX2_A	SAM links to Rfam database...	0.76	0.63	0.93	25	4344	3	0	2	1	15
3HAY_E	-	0.91	0.83	1.00	15	2263	4	0	0	4	3
3HJW_D	-	0.94	0.89	1.00	16	1637	0	0	0	0	2
3IAB_R	-	0.92	0.86	1.00	12	1023	0	0	0	0	2
3ID5_D	-	0.44	0.33	0.60	3	491	5	0	2	3	6
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...	0.76	0.67	0.88	22	4253	3	0	3	0	11
3IYQ_A	tmRNA links to Rfam database...	0.26	0.28	0.24	26	60619	83	21	60	2	68
3IZ4_A	tmRNA links to Rfam database...	0.52	0.45	0.60	60	70776	45	6	34	5	72
3IZF_C	5S_rRNA links to Rfam database...	0.59	0.52	0.68	28	6862	13	1	12	0	26
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_a	-	0.23	0.19	0.30	3	1118	7	1	6	0	13
3J0L_1	-	0.76	0.63	0.92	12	1212	2	0	1	1	7
3J0L_h	-	0.75	0.60	0.93	26	6077	4	0	2	2	17
3J0L_7	-	-0.01	0.00	0.00	0	1213	12	0	12	0	17
3J0L_2	-	0.38	0.36	0.40	12	6186	20	3	15	2	21
3J16_L	tRNA links to Rfam database...	0.50	0.40	0.63	12	2756	7	0	7	0	18
3J20_0	tRNA links to Rfam database...	0.43	0.40	0.48	12	2825	14	0	13	1	18
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J2C_O	-	0.39	0.33	0.47	21	10251	24	0	24	0	42
3J2C_M	-	0.47	0.37	0.61	77	106364	53	6	44	3	130
3J2L_3	5S_rRNA links to Rfam database...	0.59	0.51	0.69	27	7836	14	0	12	2	26
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2830	20	0	20	0	32
3JYX_3	5S_rRNA links to Rfam database...	0.63	0.63	0.63	17	6301	21	1	9	11	10
3JYX_4	5_8S_rRNA links to Rfam database...	0.31	0.30	0.31	10	12214	35	5	17	13	23
3KTW_C	-	0.39	0.35	0.45	15	4527	19	1	17	1	28
3LA5_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2465	0	0	0	0	14
3NDB_M	-	0.82	0.72	0.94	44	9133	4	0	3	1	17
3NKB_B	-	0.61	0.54	0.70	14	1996	6	0	6	0	12
3NMU_E	-	0.54	0.50	0.60	3	556	5	0	2	3	3
3NPB_A	SAM links to Rfam database...	0.77	0.63	0.94	29	6990	4	1	1	2	17
3O58_2	5S_rRNA links to Rfam database...	0.60	0.61	0.59	23	7221	18	4	12	2	15
3O58_3	5_8S_rRNA links to Rfam database...	0.34	0.34	0.34	12	12368	37	2	21	14	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...	0.67	0.56	0.80	40	12830	12	0	10	2	32
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...	0.64	0.52	0.79	22	3888	6	1	5	0	20
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...	0.39	0.32	0.48	12	3545	13	2	11	0	25
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.48	0.63	19	4723	12	1	10	1	21
3ZEX_G	-	0.52	0.45	0.61	33	16417	24	2	19	3	41
3ZEX_H	-	0.20	0.21	0.21	8	9006	31	5	26	0	30
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.63	0.91	31	6987	3	0	3	0	18
3ZEX_F	-	0.00	0.00	0.00	0	2617	11	2	9	0	12
3ZEX_E	-	0.00	0.00	0.00	0	21888	59	3	54	2	77
3ZEX_C	5_8S_rRNA links to Rfam database...	0.23	0.21	0.25	11	14152	41	1	32	8	41
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.57	0.82	31	7102	7	1	6	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11746	41	5	25	11	28
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ATO_G	-	0.32	0.30	0.38	3	520	5	1	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	1	6	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...	0.52	0.44	0.62	16	5125	10	2	8	0	20
4HXH_A	-	1.00	1.00	1.00	6	319	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 Contrafold - scored higher in this pairwise comparison

1. Total counts & total scores for Contrafold

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

Performance of RNAshapes - scored lower in this pairwise comparison

1. Total counts & total scores for RNAshapes

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