CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Sfold		McQFold
MCC	0.612	>	0.501
Average MCC ± 95% Confidence Intervals	0.768 ± 0.049	>	0.711 ± 0.055
Sensitivity	0.613	>	0.483
Positive Predictive Value	0.611	>	0.520
Total TP	3264	>	2573
Total TN	5972813	<	5973208
Total FP	2830	>	2770
Total FP CONTRA	573	=	573
Total FP INCONS	1507	<	1803
Total FP COMP	750	>	394
Total FN	2059	<	2750
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of Sfold and McQFold. 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 Sfold and McQFold).
Comparison of performance of Sfold and McQFold. 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 Sfold and McQFold).
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 Sfold and McQFold).
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 Sfold and McQFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for Sfold and McQFold. 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 Sfold and McQFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for Sfold and McQFold. 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 Sfold and McQFold).

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Performance of Sfold - scored higher in this pairwise comparison

1. Total counts & total scores for Sfold

Total Base Pair Counts
Total TP	3264
Total TN	5972813
Total FP	2830
Total FP CONTRA	573
Total FP INCONS	1507
Total FP COMP	750
Total FN	2059

Total Scores
MCC	0.612
Average MCC ± 95% Confidence Intervals	0.768 ± 0.049
Sensitivity	0.613
Positive Predictive Value	0.611
Nr of predictions	139

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2. Individual counts for Sfold [ 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	175	0	0	0	0	0
2K63_A	-	1.00	1.00	1.00	9	159	0	0	0	0	0
2K66_A	-	1.00	1.00	1.00	9	80	0	0	0	0	0
2KD8_A	-	1.00	1.00	1.00	9	99	0	0	0	0	0
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...	0.94	0.94	0.94	17	449	2	0	1	1	1
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	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	-	0.96	0.92	1.00	11	281	0	0	0	0	1
2KUR_A	K10_TLS links to Rfam database...	0.95	0.95	0.95	18	448	1	0	1	0	1
2KUU_A	K10_TLS links to Rfam database...	0.94	0.94	0.94	17	429	2	0	1	1	1
2KUV_A	K10_TLS links to Rfam database...	0.94	0.95	0.95	18	420	1	0	1	0	1
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...	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...	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...	0.46	0.39	0.58	7	516	5	0	5	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
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	-	0.95	0.90	1.00	26	2414	6	0	0	6	3
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
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
2WDL_A	-	0.50	0.50	0.50	392	1444543	429	62	325	42	396
2WRQ_Y	tRNA links to Rfam database...	0.94	0.89	1.00	8	1144	14	0	0	14	1
2WW9_F	-	0.64	0.75	0.60	6	102	4	1	3	0	2
2WW9_D	-	0.31	0.10	1.00	1	740	3	0	0	3	9
2WW9_E	-	0.89	0.80	1.00	4	168	0	0	0	0	1
2WWQ_V	tRNA links to Rfam database...	1.00	1.00	1.00	19	1185	2	0	0	2	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...	0.85	0.81	0.89	17	1110	3	0	2	1	4
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.37	0.34	0.41	12	2016	18	1	16	1	23
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	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
2YIE_X	-	0.75	0.57	1.00	4	540	0	0	0	0	3
2ZY6_A	-	0.66	0.78	0.58	7	264	5	3	2	0	2
2ZZM_B	tRNA links to Rfam database...	0.07	0.07	0.10	1	1348	17	3	6	8	14
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...	0.47	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	-	0.67	0.64	0.72	21	1790	9	0	8	1	12
3AKZ_H	tRNA links to Rfam database...	0.49	0.50	0.50	10	1107	12	3	7	2	10
3AM1_B	-	0.75	0.76	0.76	22	1437	7	3	4	0	7
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
3G4S_9	5S_rRNA links to Rfam database...	0.78	0.77	0.80	20	2711	12	2	3	7	6
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.86	0.79	0.96	22	1426	2	1	0	1	6
3HAY_E	-	1.00	1.00	1.00	14	910	7	0	0	7	0
3HJW_D	-	1.00	1.00	1.00	16	593	2	0	0	2	0
3IAB_R	-	1.00	1.00	1.00	12	373	0	0	0	0	0
3ID5_D	-	0.66	0.60	0.75	3	225	1	0	1	0	2
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...	0.69	0.68	0.70	19	1445	9	1	7	1	9
3IYQ_A	tmRNA links to Rfam database...	0.25	0.33	0.19	17	22350	86	39	34	13	34
3IZ4_A	tmRNA links to Rfam database...	0.59	0.56	0.63	53	25452	34	14	17	3	42
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	8	0	5	3	3
3J0L_a	-	0.55	0.64	0.50	7	397	8	5	2	1	4
3J0L_h	-	0.87	0.81	0.93	26	2112	4	1	1	2	6
3J0L_1	-	0.83	0.77	0.91	10	473	5	0	1	4	3
3J0L_2	-	0.44	0.42	0.48	11	2227	19	0	12	7	15
3J0L_g	-	-0.01	0.00	0.00	0	173	5	1	2	2	2
3J0L_7	-	-0.01	0.00	0.00	0	516	3	1	2	0	10
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J16_L	tRNA links to Rfam database...	0.34	0.33	0.37	7	1140	12	0	12	0	14
3J20_1	tRNA links to Rfam database...	0.75	0.75	0.75	15	1092	7	0	5	2	5
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.57	0.58	0.56	240	421940	241	31	157	53	172
3J20_0	tRNA links to Rfam database...	0.51	0.57	0.48	12	1194	14	3	10	1	9
3J2C_O	-	0.76	0.66	0.87	27	3956	9	2	2	5	14
3J2C_M	-	0.85	0.85	0.85	82	39828	51	6	9	36	14
3J2L_3	5S_rRNA links to Rfam database...	0.80	0.82	0.78	28	2984	12	1	7	4	6
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1095	16	2	14	0	20
3JYX_4	5_8S_rRNA links to Rfam database...	0.68	0.83	0.56	10	4738	23	7	1	15	2
3JYX_3	5S_rRNA links to Rfam database...	0.77	0.80	0.75	12	2362	24	0	4	20	3
3JYX_5	-	0.42	0.46	0.38	223	1968418	588	172	189	227	258
3KIY_A	-	0.53	0.51	0.56	403	1485155	373	56	266	51	383
3KTW_C	-	0.98	0.96	1.00	24	1756	8	0	0	8	1
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NDB_M	-	0.96	0.93	1.00	41	3673	4	0	0	4	3
3NKB_B	-	0.75	0.74	0.78	14	717	4	0	4	0	5
3NMU_E	-	1.00	1.00	1.00	3	213	4	0	0	4	0
3NPB_A	SAM links to Rfam database...	0.85	0.78	0.94	29	2247	7	0	2	5	8
3O58_2	5S_rRNA links to Rfam database...	0.87	0.90	0.85	28	2721	11	0	5	6	3
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.50	0.52	11	4743	18	2	8	8	11
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...	0.82	0.80	0.85	40	4793	9	2	5	2	10
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...	0.78	0.72	0.84	21	1508	4	2	2	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	2	0	0	2	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...	0.60	0.50	0.73	8	1282	7	3	0	4	8
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.63	0.64	0.64	21	1956	13	4	8	1	12
3ZEX_G	-	0.99	0.98	1.00	44	6463	15	0	0	15	1
3ZEX_F	-	0.00	0.00	0.00	0	914	7	0	0	7	4
3ZEX_C	5_8S_rRNA links to Rfam database...	0.41	0.34	0.50	10	5354	27	2	8	17	19
3ZEX_H	-	0.26	0.37	0.19	7	3589	29	18	11	0	12
3ZEX_B	-	0.37	0.39	0.35	136	420960	296	65	191	40	210
3ZEX_D	5S_rRNA links to Rfam database...	0.85	0.80	0.90	28	2765	8	0	3	5	7
3ZEX_E	-	-0.01	0.00	0.00	0	8250	56	20	34	2	34
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.25	0.19	5	4489	34	8	14	12	15
4A1C_3	5S_rRNA links to Rfam database...	0.83	0.81	0.86	30	2728	7	0	5	2	7
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ATO_G	-	0.37	0.14	1.00	1	219	0	0	0	0	6
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.57	0.33	1.00	5	491	0	0	0	0	10
4FNJ_A	-	0.91	0.83	1.00	10	240	0	0	0	0	2
4FRG_B	AdoCbl-variant links to Rfam database...	0.67	0.58	0.78	14	1184	4	3	1	0	10
4FRN_A	AdoCbl-variant links to Rfam database...	0.71	0.57	0.89	16	1830	2	2	0	0	12
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0

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Performance of McQFold - scored lower in this pairwise comparison

1. Total counts & total scores for McQFold

Total Base Pair Counts
Total TP	2573
Total TN	5973208
Total FP	2770
Total FP CONTRA	573
Total FP INCONS	1803
Total FP COMP	394
Total FN	2750

Total Scores
MCC	0.501
Average MCC ± 95% Confidence Intervals	0.711 ± 0.055
Sensitivity	0.483
Positive Predictive Value	0.520
Nr of predictions	139

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2K5Z_A	-	0.59	0.36	1.00	4	182	0	0	0	0	7
2K63_A	-	1.00	1.00	1.00	9	159	0	0	0	0	0
2K66_A	-	1.00	1.00	1.00	9	80	0	0	0	0	0
2KD8_A	-	1.00	1.00	1.00	9	99	1	0	0	1	0
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	-	0.81	0.67	1.00	6	115	1	0	0	1	3
2KMJ_A	-	1.00	1.00	1.00	11	157	1	0	0	1	0
2KPV_A	-	0.96	0.92	1.00	12	201	0	0	0	0	1
2KRL_A	-	0.75	0.83	0.68	19	1996	15	7	2	6	4
2KU0_A	-	0.86	0.75	1.00	9	283	0	0	0	0	3
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	0.94	0.94	15	355	1	0	1	0	1
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	2	0	0	2	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	1	0	0	1	0
2L3C_B	-	1.00	1.00	1.00	14	225	1	0	0	1	0
2L3E_A	-	1.00	1.00	1.00	12	228	2	0	0	2	0
2L3J_B	mir-2985-2 links to Rfam database...	0.95	0.90	1.00	27	958	0	0	0	0	3
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	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	1	4	0	7
2LDL_A	-	0.81	0.67	1.00	6	134	0	0	0	0	3
2LDT_A	-	0.79	0.64	1.00	7	155	0	0	0	0	4
2LHP_A	-	1.00	1.00	1.00	15	246	1	0	0	1	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	-	0.55	0.55	0.55	16	2411	15	5	8	2	13
2LQZ_A	-	1.00	1.00	1.00	8	124	3	0	0	3	0
2LWK_A	-	0.95	0.91	1.00	10	197	2	0	0	2	1
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	-	0.83	0.71	1.00	5	70	0	0	0	0	2
2WDL_A	-	0.37	0.37	0.36	294	1444515	545	84	429	32	494
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	14	0	0	14	0
2WW9_F	-	0.86	0.75	1.00	6	106	1	0	0	1	2
2WW9_D	-	0.44	0.40	0.50	4	733	9	4	0	5	6
2WW9_E	-	-0.03	0.00	0.00	0	168	5	0	4	1	5
2WWQ_V	tRNA links to Rfam database...	0.00	0.00	0.00	0	1204	0	0	0	0	19
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.33	0.36	0.31	4	1822	27	2	7	18	7
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...	0.27	0.26	0.30	9	2015	22	0	21	1	26
2Y8W_B	-	1.00	1.00	1.00	6	82	2	0	0	2	0
2Y9C_V	-	0.72	0.72	0.72	13	888	8	0	5	3	5
2YIE_Z	-	0.53	0.63	0.45	5	591	6	4	2	0	3
2YIE_X	-	0.53	0.57	0.50	4	536	6	1	3	2	3
2ZY6_A	-	0.66	0.78	0.58	7	264	5	3	2	0	2
2ZZM_B	tRNA links to Rfam database...	0.18	0.20	0.19	3	1342	22	4	9	9	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...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3ADB_C	-	0.98	0.97	1.00	32	1787	1	0	0	1	1
3AKZ_H	tRNA links to Rfam database...	0.78	0.80	0.76	16	1106	7	2	3	2	4
3AM1_B	-	1.00	1.00	1.00	29	1437	1	0	0	1	0
3AMU_B	tRNA links to Rfam database...	0.86	0.79	0.94	15	1141	4	0	1	3	4
3DW4_A	-	-0.03	0.00	0.00	0	137	3	0	3	0	6
3G4S_9	5S_rRNA links to Rfam database...	0.39	0.42	0.37	11	2706	22	6	13	3	15
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.56	0.57	0.57	16	1421	13	4	8	1	12
3HAY_E	-	1.00	1.00	1.00	14	910	4	0	0	4	0
3HJW_D	-	0.94	0.94	0.94	15	593	3	0	1	2	1
3IAB_R	-	1.00	1.00	1.00	12	373	0	0	0	0	0
3ID5_D	-	0.66	0.60	0.75	3	225	6	0	1	5	2
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...	0.21	0.21	0.24	6	1447	19	2	17	0	22
3IYQ_A	tmRNA links to Rfam database...	0.22	0.31	0.15	16	22335	100	45	44	11	35
3IZ4_A	tmRNA links to Rfam database...	0.46	0.46	0.47	44	25442	56	14	36	6	51
3IZF_C	5S_rRNA links to Rfam database...	0.85	0.83	0.88	29	2607	7	0	4	3	6
3J0L_a	-	0.21	0.18	0.29	2	404	6	3	2	1	9
3J0L_h	-	0.75	0.66	0.88	21	2116	3	0	3	0	11
3J0L_1	-	0.73	0.62	0.89	8	475	4	0	1	3	5
3J0L_2	-	0.29	0.31	0.30	8	2223	21	1	18	2	18
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_7	-	-0.02	0.00	0.00	0	509	10	2	8	0	10
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	0	0	0	0	4
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.55	0.56	0.55	231	421948	234	41	148	45	181
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	1	5
3J2C_O	-	0.62	0.61	0.64	25	3948	17	3	11	3	16
3J2C_M	-	0.38	0.44	0.34	42	39801	95	33	49	13	54
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.68	0.74	23	2989	11	0	8	3	11
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1091	20	4	16	0	20
3JYX_4	5_8S_rRNA links to Rfam database...	0.35	0.58	0.22	7	4724	33	17	8	8	5
3JYX_3	5S_rRNA links to Rfam database...	0.28	0.40	0.20	6	2348	24	17	7	0	9
3JYX_5	-	0.00	0.00	0.00	0	1969002	0	0	0	0	481
3KIY_A	-	0.38	0.38	0.38	302	1485090	544	83	405	56	484
3KTW_C	-	0.52	0.52	0.54	13	1756	17	2	9	6	12
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	5	0	1	4	2
3NKB_B	-	0.42	0.42	0.44	8	717	10	2	8	0	11
3NMU_E	-	0.57	0.33	1.00	1	215	3	0	0	3	2
3NPB_A	SAM links to Rfam database...	0.90	0.81	1.00	30	2248	5	0	0	5	7
3O58_2	5S_rRNA links to Rfam database...	0.93	0.87	1.00	27	2727	2	0	0	2	4
3O58_3	5_8S_rRNA links to Rfam database...	0.30	0.36	0.25	8	4732	27	15	9	3	14
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...	0.83	0.80	0.87	40	4794	9	2	4	3	10
3R4F_A	-	1.00	1.00	1.00	22	884	2	0	0	2	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...	0.82	0.83	0.83	24	1504	5	1	4	0	5
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	2	0	0	2	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	-	0.95	0.91	1.00	20	1256	2	0	0	2	2
3UZL_B	tRNA links to Rfam database...	0.62	0.75	0.52	12	1270	17	8	3	6	4
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.49	0.45	0.54	15	1961	14	1	12	1	18
3ZEX_G	-	0.36	0.40	0.34	18	6454	40	11	24	5	27
3ZEX_F	-	0.00	0.00	0.00	0	910	9	0	4	5	4
3ZEX_C	5_8S_rRNA links to Rfam database...	0.33	0.34	0.32	10	5343	25	4	17	4	19
3ZEX_H	-	0.27	0.37	0.21	7	3591	30	14	13	3	12
3ZEX_B	-	0.12	0.14	0.12	47	420944	379	78	283	18	299
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.66	0.88	23	2770	6	1	2	3	12
3ZEX_E	-	0.00	0.00	0.00	0	8256	53	17	31	5	34
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	33	11	16	6	15
4A1C_3	5S_rRNA links to Rfam database...	0.28	0.30	0.28	11	2724	30	4	24	2	26
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
4ATO_G	-	-0.03	0.00	0.00	0	215	5	0	5	0	7
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FNJ_A	-	-0.04	0.00	0.00	0	243	7	0	7	0	12
4FRG_B	AdoCbl-variant links to Rfam database...	0.93	0.88	1.00	21	1181	0	0	0	0	3
4FRN_A	AdoCbl-variant links to Rfam database...	0.82	0.71	0.95	20	1827	1	1	0	0	8
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 Sfold - scored higher in this pairwise comparison

1. Total counts & total scores for Sfold

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

Performance of McQFold - scored lower in this pairwise comparison

1. Total counts & total scores for McQFold

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