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		Pknots
MCC	0.673	>	0.601
Average MCC ± 95% Confidence Intervals	0.703 ± 0.048	>	0.657 ± 0.054
Sensitivity	0.579	>	0.545
Positive Predictive Value	0.787	>	0.670
Total TP	1767	>	1663
Total TN	346090	>	345853
Total FP	605	<	920
Total FP CONTRA	55	<	104
Total FP INCONS	423	<	715
Total FP COMP	127	>	101
Total FN	1286	<	1390
P-value	3.56938820447e-08

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Performance plots

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

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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	1767
Total TN	346090
Total FP	605
Total FP CONTRA	55
Total FP INCONS	423
Total FP COMP	127
Total FN	1286

Total Scores
MCC	0.673
Average MCC ± 95% Confidence Intervals	0.703 ± 0.048
Sensitivity	0.579
Positive Predictive Value	0.787
Nr of predictions	130

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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
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	-	0.89	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
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_E	-	0.53	0.29	1.00	4	557	0	0	0	0	10
2WW9_D	-	0.29	0.12	0.75	3	1949	1	0	1	0	23
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
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.61	0.83	33	6863	7	0	7	0	21
3J0L_h	-	0.75	0.60	0.93	26	6077	4	0	2	2	17
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_a	-	0.51	0.50	0.53	8	1113	7	3	4	0	8
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_1	-	0.76	0.63	0.92	12	1212	3	0	1	2	7
3J0L_7	-	-0.01	0.00	0.00	0	1222	3	0	3	0	17
3J16_L	tRNA links to Rfam database...	0.29	0.23	0.37	7	2756	12	0	12	0	23
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...	0.73	0.70	0.76	16	2905	6	0	5	1	7
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
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_3	5_8S_rRNA links to Rfam database...	0.43	0.34	0.55	12	12381	17	0	10	7	23
3O58_2	5S_rRNA links to Rfam database...	0.74	0.74	0.74	28	7222	11	3	7	1	10
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_H	-	0.19	0.18	0.19	7	9009	29	5	24	0	31
3ZEX_D	5S_rRNA links to Rfam database...	0.74	0.63	0.86	31	6985	5	0	5	0	18
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
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	1	5	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11751	34	2	23	9	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	-	0.31	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 Pknots - scored lower in this pairwise comparison

1. Total counts & total scores for Pknots

Total Base Pair Counts
Total TP	1663
Total TN	345853
Total FP	920
Total FP CONTRA	104
Total FP INCONS	715
Total FP COMP	101
Total FN	1390

Total Scores
MCC	0.601
Average MCC ± 95% Confidence Intervals	0.657 ± 0.054
Sensitivity	0.545
Positive Predictive Value	0.670
Nr of predictions	130

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2K5Z_A	-	0.90	0.82	1.00	9	397	0	0	0	0	2
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	-	0.11	0.10	0.17	2	618	10	0	10	0	18
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	0	0	0	0	0
2KPV_A	-	0.96	0.92	1.00	12	549	0	0	0	0	1
2KRL_A	-	0.67	0.58	0.79	23	5122	9	2	4	3	17
2KU0_A	-	-0.02	0.00	0.00	0	693	10	0	10	0	16
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	-	-0.02	0.00	0.00	0	346	5	0	5	0	10
2KZL_A	-	0.59	0.53	0.67	10	1470	5	1	4	0	9
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	-	0.87	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...	0.92	0.90	0.95	18	971	1	0	1	0	2
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	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.79	0.75	0.83	15	1522	3	1	2	0	5
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	-	0.44	0.44	0.45	17	6067	22	4	17	1	22
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LWK_A	-	0.33	0.23	0.50	3	490	3	0	3	0	10
2RP0_A	-	0.66	0.58	0.78	7	342	2	1	1	0	5
2RPT_A	-	1.00	1.00	1.00	7	183	0	0	0	0	0
2RRC_A	-	0.77	0.60	1.00	6	225	0	0	0	0	4
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	12	5	3	4	7
2WW9_F	-	0.59	0.60	0.60	6	290	4	0	4	0	4
2WW9_E	-	0.39	0.29	0.57	4	554	3	0	3	0	10
2WW9_D	-	0.35	0.31	0.42	8	1934	11	2	9	0	18
2WWQ_V	tRNA links to Rfam database...	0.24	0.21	0.29	6	2905	16	1	14	1	22
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.23	0.25	0.22	5	4537	31	1	17	13	15
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...	0.32	0.31	0.34	13	5113	25	1	24	0	29
2Y8W_B	-	1.00	1.00	1.00	6	184	1	0	0	1	0
2Y9C_V	-	0.59	0.50	0.71	12	2261	6	1	4	1	12
2YIE_Z	-	-0.01	0.00	0.00	0	1525	15	3	12	0	12
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...	0.20	0.19	0.23	6	3460	20	2	18	0	26
2ZZN_D	tRNA links to Rfam database...	0.86	0.78	0.95	21	2463	1	0	1	0	6
3A2K_C	tRNA links to Rfam database...	0.45	0.43	0.48	12	2901	13	2	11	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...	0.84	0.75	0.95	21	2679	1	1	0	0	7
3AM1_B	-	0.91	0.83	1.00	29	3211	0	0	0	0	6
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	2	0	0	2	7
3DW4_A	-	0.70	0.50	1.00	5	346	0	0	0	0	5
3G4S_9	5S_rRNA links to Rfam database...	0.25	0.21	0.31	12	7342	27	0	27	0	45
3GCA_A	-	0.35	0.24	0.57	4	521	3	0	3	0	13
3GX2_A	SAM links to Rfam database...	0.47	0.40	0.55	16	4342	14	1	12	1	24
3HAY_E	-	0.86	0.83	0.88	15	2261	5	0	2	3	3
3HJW_D	-	0.94	0.89	1.00	16	1637	3	0	0	3	2
3IAB_R	-	0.86	0.86	0.86	12	1021	4	1	1	2	2
3ID5_D	-	-0.01	0.00	0.00	0	491	5	1	4	0	9
3IVN_B	Purine links to Rfam database...	0.78	0.65	0.95	20	2325	1	0	1	0	11
3IWN_A	c-di-GMP-I links to Rfam database...	0.21	0.18	0.25	6	4254	18	1	17	0	27
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.61	0.80	33	6862	8	1	7	0	21
3J0L_h	-	0.58	0.49	0.70	21	6075	11	0	9	2	22
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_a	-	0.35	0.31	0.42	5	1116	7	1	6	0	11
3J0L_2	-	0.36	0.36	0.36	12	6183	23	3	18	2	21
3J0L_g	-	-0.01	0.00	0.00	0	460	5	2	3	0	4
3J0L_1	-	0.65	0.47	0.90	9	1215	2	0	1	1	10
3J0L_7	-	0.28	0.29	0.29	5	1208	12	0	12	0	12
3J16_L	tRNA links to Rfam database...	0.34	0.30	0.41	9	2753	13	0	13	0	21
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	1	0	0	1	9
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.51	0.75	27	7839	12	0	9	3	26
3JYV_7	tRNA links to Rfam database...	0.81	0.66	1.00	21	2829	0	0	0	0	11
3JYX_4	5_8S_rRNA links to Rfam database...	0.18	0.21	0.16	7	12203	41	13	23	5	26
3JYX_3	5S_rRNA links to Rfam database...	0.34	0.37	0.31	10	6296	24	9	13	2	17
3KTW_C	-	0.49	0.44	0.56	19	4526	16	2	13	1	24
3LA5_A	Purine links to Rfam database...	0.80	0.65	1.00	22	2463	0	0	0	0	12
3NDB_M	-	0.77	0.69	0.88	42	9132	7	1	5	1	19
3NKB_B	-	0.55	0.50	0.62	13	1995	8	0	8	0	13
3NMU_E	-	0.54	0.50	0.60	3	556	5	0	2	3	3
3NPB_A	SAM links to Rfam database...	0.76	0.67	0.86	31	6985	8	1	4	3	15
3O58_3	5_8S_rRNA links to Rfam database...	0.27	0.31	0.24	11	12357	38	11	24	3	24
3O58_2	5S_rRNA links to Rfam database...	0.83	0.74	0.93	28	7230	3	0	2	1	10
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...	0.54	0.44	0.65	32	12831	19	0	17	2	40
3R4F_A	-	0.92	0.88	0.96	22	2122	1	0	1	0	3
3R9X_C	-	0.73	0.70	0.78	7	586	5	0	2	3	3
3RKF_A	Purine links to Rfam database...	0.77	0.62	0.95	21	2189	1	0	1	0	13
3SD1_A	THF links to Rfam database...	0.65	0.52	0.81	22	3889	5	0	5	0	20
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	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	-	0.26	0.22	0.32	8	3135	17	0	17	0	29
3UZL_B	tRNA links to Rfam database...	0.75	0.59	0.96	22	3547	1	0	1	0	15
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.71	0.63	0.81	25	4722	7	0	6	1	15
3ZEX_H	-	0.20	0.21	0.20	8	9005	32	5	27	0	30
3ZEX_D	5S_rRNA links to Rfam database...	0.27	0.24	0.30	12	6981	28	0	28	0	37
3ZEX_G	-	0.36	0.32	0.41	24	16413	37	3	31	3	50
3ZEX_F	-	0.00	0.00	0.00	0	2619	12	2	7	3	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.07	0.08	0.07	4	14141	54	4	47	3	48
4A1C_3	5S_rRNA links to Rfam database...	0.25	0.22	0.29	12	7099	29	1	28	0	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.24	0.25	8	11749	36	3	21	12	25
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.17	0.14	0.21	6	4343	23	1	21	1	36
4ATO_G	-	0.30	0.30	0.33	3	519	6	2	4	0	7
4ENB_A	crcB links to Rfam database...	0.83	0.79	0.88	15	1258	2	1	1	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	585	10	0	10	0	16
4FRG_B	AdoCbl-variant links to Rfam database...	0.48	0.38	0.63	12	3467	7	0	7	0	20
4FRN_A	AdoCbl-variant links to Rfam database...	0.51	0.42	0.63	15	5127	9	1	8	0	21
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 Pknots - scored lower in this pairwise comparison

1. Total counts & total scores for Pknots

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