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	0.508	>	0.415
Average MCC ± 95% Confidence Intervals	0.680 ± 0.047	>	0.637 ± 0.053
Sensitivity	0.431	>	0.332
Positive Predictive Value	0.598	>	0.518
Total TP	3506	>	2702
Total TN	15816674	<	15817317
Total FP	2588	<	2641
Total FP CONTRA	311	>	214
Total FP INCONS	2041	<	2299
Total FP COMP	236	>	128
Total FN	4633	<	5437
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	3506
Total TN	15816674
Total FP	2588
Total FP CONTRA	311
Total FP INCONS	2041
Total FP COMP	236
Total FN	4633

Total Scores
MCC	0.508
Average MCC ± 95% Confidence Intervals	0.680 ± 0.047
Sensitivity	0.431
Positive Predictive Value	0.598
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	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...	0.92	0.89	0.94	17	1110	2	0	1	1	2
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...	0.90	0.86	0.95	18	1109	1	0	1	0	3
2KUU_A	K10_TLS links to Rfam database...	0.87	0.81	0.94	17	1110	2	0	1	1	4
2KUV_A	K10_TLS links to Rfam database...	0.88	0.82	0.95	18	1109	1	0	1	0	4
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...	0.94	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_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	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...	0.97	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...	0.45	0.35	0.58	7	1528	5	0	5	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
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	-	0.89	0.79	1.00	31	6074	1	0	0	1	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
2WDL_A	-	0.41	0.34	0.50	410	3937401	411	25	385	1	794
2WRQ_Y	tRNA links to Rfam database...	0.53	0.53	0.53	9	2833	13	5	3	5	8
2WW9_F	-	0.69	0.70	0.70	7	290	3	0	3	0	3
2WW9_D	-	0.29	0.12	0.75	3	1949	1	0	1	0	23
2WW9_E	-	0.53	0.29	1.00	4	557	0	0	0	0	10
2WWQ_V	tRNA links to Rfam database...	0.80	0.68	0.95	19	2906	2	0	1	1	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...	0.77	0.67	0.90	18	2830	2	0	2	0	9
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.36	0.31	0.43	13	5121	17	1	16	0	29
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_Z	-	-0.01	0.00	0.00	0	1525	15	3	12	0	12
2YIE_X	-	0.58	0.33	1.00	4	1374	0	0	0	0	8
2ZY6_A	-	0.58	0.58	0.58	7	691	5	1	4	0	5
2ZZM_B	tRNA links to Rfam database...	0.12	0.09	0.17	3	3468	15	0	15	0	29
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...	0.42	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	-	0.62	0.55	0.70	21	4156	9	0	9	0	17
3AKZ_H	tRNA links to Rfam database...	0.44	0.39	0.50	11	2679	11	2	9	0	17
3AM1_B	-	0.69	0.63	0.76	22	3211	7	1	6	0	13
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	345	6	0	6	0	10
3G4S_9	5S_rRNA links to Rfam database...	0.51	0.39	0.69	22	7349	10	1	9	0	35
3GCA_A	-	0.54	0.29	1.00	5	523	0	0	0	0	12
3GX2_A	SAM links to Rfam database...	0.72	0.55	0.96	22	4348	2	0	1	1	18
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	-	0.92	0.86	1.00	12	1023	0	0	0	0	2
3ID5_D	-	0.49	0.33	0.75	3	492	1	0	1	0	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...	0.63	0.58	0.70	19	4251	9	0	8	1	14
3IYQ_A	tmRNA links to Rfam database...	0.33	0.34	0.32	32	60627	71	19	48	4	62
3IZ4_A	tmRNA links to Rfam database...	0.52	0.42	0.65	56	70790	31	3	27	1	76
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.61	0.83	33	6863	7	0	7	0	21
3J0L_a	-	0.51	0.50	0.53	8	1113	7	3	4	0	8
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	3	0	1	2	7
3J0L_2	-	0.36	0.33	0.39	11	6188	19	2	15	2	22
3J0L_g	-	-0.01	0.00	0.00	0	460	5	1	4	0	4
3J0L_7	-	-0.01	0.00	0.00	0	1222	3	0	3	0	17
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J16_L	tRNA links to Rfam database...	0.29	0.23	0.37	7	2756	12	0	12	0	23
3J20_1	tRNA links to Rfam database...	0.73	0.70	0.76	16	2905	6	0	5	1	7
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.47	0.41	0.55	261	1116287	220	14	203	3	372
3J20_0	tRNA links to Rfam database...	0.43	0.40	0.48	12	2825	14	0	13	1	18
3J2C_O	-	0.64	0.48	0.86	30	10261	6	0	5	1	33
3J2C_M	-	0.63	0.49	0.80	102	106363	31	3	23	5	105
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.53	0.74	28	7837	12	0	10	2	25
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2834	16	0	16	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.35	0.30	0.42	10	12222	23	3	11	9	23
3JYX_3	5S_rRNA links to Rfam database...	0.62	0.63	0.61	17	6300	19	1	10	8	10
3JYX_5	-	0.35	0.32	0.39	286	5022127	525	142	310	73	607
3KIY_A	-	0.43	0.34	0.55	424	4053360	352	20	324	8	817
3KTW_C	-	0.74	0.63	0.87	27	4529	5	2	2	1	16
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NDB_M	-	0.81	0.69	0.95	42	9136	3	0	2	1	19
3NKB_B	-	0.64	0.54	0.78	14	1998	4	0	4	0	12
3NMU_E	-	0.61	0.50	0.75	3	557	4	0	1	3	3
3NPB_A	SAM links to Rfam database...	0.77	0.65	0.91	30	6988	6	1	2	3	16
3O58_2	5S_rRNA links to Rfam database...	0.74	0.74	0.74	28	7222	11	3	7	1	10
3O58_3	5_8S_rRNA links to Rfam database...	0.43	0.34	0.55	12	12381	17	0	10	7	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...	0.69	0.56	0.85	40	12833	9	0	7	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...	0.65	0.50	0.84	21	3891	4	1	3	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	2	0	0	2	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...	0.51	0.32	0.80	12	3555	3	2	1	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...	0.57	0.53	0.64	21	4720	13	1	11	1	19
3ZEX_G	-	0.78	0.68	0.91	50	16416	9	0	5	4	24
3ZEX_F	-	0.00	0.00	0.00	0	2623	7	2	3	2	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.21	0.48	11	14173	26	1	11	14	41
3ZEX_H	-	0.19	0.18	0.19	7	9009	29	5	24	0	31
3ZEX_B	-	0.31	0.27	0.36	152	1071959	280	27	242	11	406
3ZEX_D	5S_rRNA links to Rfam database...	0.74	0.63	0.86	31	6985	5	0	5	0	18
3ZEX_E	-	0.00	0.00	0.00	0	21891	56	3	51	2	77
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11751	34	2	23	9	28
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	1	5	0	23
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	-	0.31	0.10	1.00	1	527	0	0	0	0	9
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...	0.51	0.26	1.00	5	1321	0	0	0	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...	0.62	0.47	0.83	15	3468	3	1	2	0	17
4FRN_A	AdoCbl-variant links to Rfam database...	0.63	0.44	0.89	16	5133	2	2	0	0	20
4HXH_A	-	1.00	1.00	1.00	6	319	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	2702
Total TN	15817317
Total FP	2641
Total FP CONTRA	214
Total FP INCONS	2299
Total FP COMP	128
Total FN	5437

Total Scores
MCC	0.415
Average MCC ± 95% Confidence Intervals	0.637 ± 0.053
Sensitivity	0.332
Positive Predictive Value	0.518
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	-	0.60	0.36	1.00	4	402	0	0	0	0	7
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	1	0	0	1	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...	0.89	0.79	1.00	15	1113	1	0	0	1	4
2KEZ_A	-	0.89	0.80	1.00	8	268	0	0	0	0	2
2KFC_A	-	0.49	0.25	1.00	5	625	0	0	0	0	15
2KGP_A	-	0.81	0.67	1.00	6	294	1	0	0	1	3
2KMJ_A	-	1.00	1.00	1.00	11	367	1	0	0	1	0
2KPV_A	-	0.96	0.92	1.00	12	549	0	0	0	0	1
2KRL_A	-	0.59	0.53	0.68	21	5120	13	3	7	3	19
2KU0_A	-	0.75	0.56	1.00	9	694	0	0	0	0	7
2KUR_A	K10_TLS links to Rfam database...	0.87	0.76	1.00	16	1112	0	0	0	0	5
2KUU_A	K10_TLS links to Rfam database...	0.84	0.71	1.00	15	1113	1	0	0	1	6
2KUV_A	K10_TLS links to Rfam database...	0.85	0.73	1.00	16	1112	0	0	0	0	6
2KUW_A	K10_TLS links to Rfam database...	0.87	0.76	1.00	16	1112	0	0	0	0	5
2KX8_A	7SK links to Rfam database...	0.88	0.83	0.94	15	845	1	0	1	0	3
2KXM_A	-	0.70	0.50	1.00	5	346	0	0	0	0	5
2KZL_A	-	0.86	0.74	1.00	14	1471	1	0	0	1	5
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L2K_A	-	0.97	0.95	1.00	18	843	0	0	0	0	1
2L3C_B	-	0.94	0.88	1.00	15	546	0	0	0	0	2
2L3E_A	-	1.00	1.00	1.00	13	582	1	0	0	1	0
2L3J_B	mir-2985-2 links to Rfam database...	0.89	0.79	1.00	27	2458	0	0	0	0	7
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	-	0.46	0.26	0.83	5	624	1	0	1	0	14
2LBS_A	-	1.00	1.00	1.00	14	482	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	5	0	5	0	9
2LDL_A	-	0.73	0.55	1.00	6	345	0	0	0	0	5
2LDT_A	-	0.68	0.47	1.00	7	458	0	0	0	0	8
2LHP_A	-	1.00	1.00	1.00	16	650	0	0	0	0	0
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	-	0.51	0.46	0.58	18	6074	13	2	11	0	21
2LQZ_A	-	0.91	0.91	0.91	10	340	1	1	0	0	1
2LWK_A	-	0.83	0.77	0.91	10	485	2	0	1	1	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
2WDL_A	-	0.31	0.26	0.37	308	3937383	531	27	503	1	896
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2WW9_F	-	0.71	0.60	0.86	6	293	1	0	1	0	4
2WW9_D	-	0.32	0.23	0.46	6	1940	7	2	5	0	20
2WW9_E	-	-0.01	0.00	0.00	0	556	5	0	5	0	14
2WWQ_V	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	28
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.31	0.30	0.33	6	4542	25	1	11	13	14
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.27	0.24	0.32	10	5120	21	0	21	0	32
2Y8W_B	-	1.00	1.00	1.00	6	184	2	0	0	2	0
2Y9C_V	-	0.59	0.54	0.65	13	2258	8	1	6	1	11
2YIE_Z	-	0.43	0.42	0.45	5	1529	6	3	3	0	7
2YIE_X	-	0.36	0.33	0.40	4	1368	6	2	4	0	8
2ZY6_A	-	0.58	0.58	0.58	7	691	5	1	4	0	5
2ZZM_B	tRNA links to Rfam database...	0.21	0.19	0.24	6	3461	19	2	17	0	26
2ZZN_D	tRNA links to Rfam database...	0.84	0.78	0.91	21	2462	2	0	2	0	6
3A2K_C	tRNA links to Rfam database...	0.86	0.75	1.00	21	2905	0	0	0	0	7
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	1	0	0	1	6
3AKZ_H	tRNA links to Rfam database...	0.68	0.61	0.77	17	2679	6	1	4	1	11
3AM1_B	-	0.91	0.83	1.00	29	3211	1	0	0	1	6
3AMU_B	tRNA links to Rfam database...	0.75	0.59	0.94	16	2986	3	0	1	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...	0.27	0.21	0.36	12	7348	21	1	20	0	45
3GCA_A	-	0.54	0.29	1.00	5	523	0	0	0	0	12
3GX2_A	SAM links to Rfam database...	0.47	0.40	0.57	16	4343	13	1	11	1	24
3HAY_E	-	0.91	0.83	1.00	15	2263	3	0	0	3	3
3HJW_D	-	0.88	0.83	0.94	15	1637	3	0	1	2	3
3IAB_R	-	0.92	0.86	1.00	12	1023	0	0	0	0	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...	0.20	0.18	0.24	6	4253	19	2	17	0	27
3IYQ_A	tmRNA links to Rfam database...	0.28	0.31	0.26	29	60614	87	19	64	4	65
3IZ4_A	tmRNA links to Rfam database...	0.42	0.36	0.49	47	70780	53	6	43	4	85
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	6867	6	0	6	0	24
3J0L_a	-	0.26	0.19	0.38	3	1120	5	1	4	0	13
3J0L_h	-	0.65	0.49	0.88	21	6081	3	0	3	0	22
3J0L_1	-	0.65	0.47	0.90	9	1215	3	0	1	2	10
3J0L_2	-	0.26	0.24	0.30	8	6189	21	0	19	2	25
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_7	-	-0.01	0.00	0.00	0	1215	10	0	10	0	17
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.46	0.39	0.54	249	1116304	216	8	204	4	384
3J20_0	tRNA links to Rfam database...	0.66	0.57	0.77	17	2828	6	1	4	1	13
3J2C_O	-	0.53	0.43	0.66	27	10255	15	1	13	1	36
3J2C_M	-	0.31	0.25	0.38	51	106357	86	12	71	3	156
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.43	0.72	23	7843	11	0	9	2	30
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2830	20	0	20	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.20	0.21	0.19	7	12210	33	8	21	4	26
3JYX_3	5S_rRNA links to Rfam database...	0.21	0.22	0.20	6	6298	24	9	15	0	21
3JYX_5	-	0.00	0.00	0.00	0	5022865	0	0	0	0	893
3KIY_A	-	0.31	0.26	0.38	317	4053291	529	22	498	9	924
3KTW_C	-	0.36	0.30	0.45	13	4531	17	1	15	1	30
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NDB_M	-	0.81	0.70	0.93	43	9134	4	1	2	1	18
3NKB_B	-	0.36	0.31	0.44	8	1998	10	1	9	0	18
3NMU_E	-	0.41	0.17	1.00	1	560	3	0	0	3	5
3NPB_A	SAM links to Rfam database...	0.81	0.67	0.97	31	6989	4	1	0	3	15
3O58_2	5S_rRNA links to Rfam database...	0.83	0.71	0.96	27	7232	2	0	1	1	11
3O58_3	5_8S_rRNA links to Rfam database...	0.26	0.26	0.26	9	12368	26	10	16	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	0	0	0	0	1
3PDR_A	ykoK links to Rfam database...	0.69	0.56	0.87	40	12834	9	0	6	3	32
3R4F_A	-	0.96	0.92	1.00	23	2122	1	0	0	1	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...	0.71	0.60	0.86	25	3887	4	0	4	0	17
3SIU_F	-	0.73	0.55	1.00	6	372	0	0	0	0	5
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	2	0	0	2	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	-	0.73	0.57	0.95	21	3138	1	0	1	0	16
3UZL_B	tRNA links to Rfam database...	0.45	0.41	0.52	15	3541	14	0	14	0	22
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.44	0.38	0.54	15	4725	14	0	13	1	25
3ZEX_G	-	0.31	0.27	0.36	20	16416	38	1	34	3	54
3ZEX_F	-	0.00	0.00	0.00	0	2619	9	2	7	0	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.27	0.21	0.34	11	14164	24	2	19	3	41
3ZEX_H	-	0.21	0.21	0.22	8	9009	29	6	22	1	30
3ZEX_B	-	0.11	0.09	0.13	53	1071960	373	32	335	6	505
3ZEX_D	5S_rRNA links to Rfam database...	0.69	0.53	0.90	26	6992	3	1	2	0	23
3ZEX_E	-	0.00	0.00	0.00	0	21894	53	4	47	2	77
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11748	33	5	23	5	28
4A1C_3	5S_rRNA links to Rfam database...	0.25	0.22	0.29	12	7099	29	1	28	0	42
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
4ATO_G	-	-0.01	0.00	0.00	0	523	5	0	5	0	10
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4
4FNJ_A	-	-0.02	0.00	0.00	0	588	7	0	7	0	16
4FRG_B	AdoCbl-variant links to Rfam database...	0.81	0.66	1.00	21	3465	0	0	0	0	11
4FRN_A	AdoCbl-variant links to Rfam database...	0.73	0.56	0.95	20	5130	1	1	0	0	16
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 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 ]