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		MaxExpect
MCC	0.554	>	0.549
Average MCC ± 95% Confidence Intervals	0.654 ± 0.050	>	0.644 ± 0.053
Sensitivity	0.455	<	0.477
Positive Predictive Value	0.674	>	0.631
Total TP	2785	<	2920
Total TN	6889574	>	6889079
Total FP	1489	<	1897
Total FP CONTRA	145	<	166
Total FP INCONS	1201	<	1540
Total FP COMP	143	<	191
Total FN	3331	>	3196
P-value	3.09925167801e-06

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Performance plots

Comparison of performance of CentroidFold and MaxExpect. 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 MaxExpect).
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 MaxExpect).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidFold and MaxExpect. 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 MaxExpect).

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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	2785
Total TN	6889574
Total FP	1489
Total FP CONTRA	145
Total FP INCONS	1201
Total FP COMP	143
Total FN	3331

Total Scores
MCC	0.554
Average MCC ± 95% Confidence Intervals	0.654 ± 0.050
Sensitivity	0.455
Positive Predictive Value	0.674
Nr of predictions	130

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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
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
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
3A2K_C	tRNA links to Rfam database...	0.44	0.43	0.46	12	2900	14	2	12	0	16
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
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_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_g	-	0.00	0.00	0.00	0	465	0	0	0	0	4
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
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.56	0.48	0.67	303	1116310	158	8	144	6	330
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_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7485	21	2	16	3	33
3J3E_7	5S_rRNA links to Rfam database...	0.46	0.37	0.59	20	7106	14	1	13	0	34
3J3F_8	5_8S_rRNA links to Rfam database...	0.34	0.33	0.34	12	12211	34	4	19	11	24
3J3F_7	5S_rRNA links to Rfam database...	0.20	0.18	0.23	9	7221	30	1	29	0	41
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_3	5S_rRNA links to Rfam database...	0.29	0.30	0.30	8	6301	20	8	11	1	19
3JYX_4	5_8S_rRNA links to Rfam database...	0.23	0.21	0.25	7	12218	25	5	16	4	26
3KIY_A	-	0.53	0.41	0.69	505	4053393	246	24	206	16	736
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_E	-	0.00	0.00	0.00	0	21895	52	3	47	2	77
3ZEX_D	5S_rRNA links to Rfam database...	0.73	0.59	0.91	29	6989	3	0	3	0	20
3ZEX_B	-	0.23	0.16	0.34	87	1072121	178	9	163	6	471
3ZEX_H	-	0.19	0.18	0.21	7	9011	27	4	23	0	31
3ZEX_F	-	0.00	0.00	0.00	0	2619	9	2	7	0	12
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	23	1	20	2	18
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.56	0.81	30	7103	7	1	6	0	24
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11752	29	5	19	5	28
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 MaxExpect - scored lower in this pairwise comparison

1. Total counts & total scores for MaxExpect

Total Base Pair Counts
Total TP	2920
Total TN	6889079
Total FP	1897
Total FP CONTRA	166
Total FP INCONS	1540
Total FP COMP	191
Total FN	3196

Total Scores
MCC	0.549
Average MCC ± 95% Confidence Intervals	0.644 ± 0.053
Sensitivity	0.477
Positive Predictive Value	0.631
Nr of predictions	130

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2. Individual counts for MaxExpect [ 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...	0.92	0.89	0.94	17	1110	2	0	1	1	2
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	-	-0.02	0.00	0.00	0	694	9	0	9	0	16
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	-	0.83	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...	0.98	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...	0.97	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	0.74	0.88	29	6072	6	0	4	2	10
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	-	0.88	0.85	0.92	11	484	1	0	1	0	2
2M58_A	-	-0.01	0.00	0.00	0	1640	13	0	13	0	17
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
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	-	0.14	0.12	0.19	3	1937	13	0	13	0	23
2WW9_E	-	-0.01	0.00	0.00	0	556	5	0	5	0	14
2WWQ_V	tRNA links to Rfam database...	0.76	0.64	0.90	18	2906	3	0	2	1	10
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.51	0.50	0.53	10	4541	24	0	9	15	10
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...	0.25	0.24	0.27	10	5114	27	1	26	0	32
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	-	0.36	0.33	0.40	4	1368	6	2	4	0	8
2YIE_Z	-	-0.01	0.00	0.00	0	1525	15	3	12	0	12
3A2K_C	tRNA links to Rfam database...	0.42	0.39	0.46	11	2902	13	2	11	0	17
3ADB_C	-	0.80	0.74	0.88	28	4154	4	0	4	0	10
3AKZ_H	tRNA links to Rfam database...	0.84	0.75	0.95	21	2679	1	1	0	0	7
3AM1_B	-	0.78	0.71	0.86	25	3211	4	0	4	0	10
3AMU_B	tRNA links to Rfam database...	0.64	0.59	0.70	16	2980	9	0	7	2	11
3GX2_A	SAM links to Rfam database...	0.77	0.63	0.96	25	4345	2	0	1	1	15
3IAB_R	-	0.92	0.86	1.00	12	1023	0	0	0	0	2
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...	0.74	0.67	0.81	22	4251	6	0	5	1	11
3IYQ_A	tmRNA links to Rfam database...	0.29	0.31	0.27	29	60617	84	19	61	4	65
3IZ4_A	tmRNA links to Rfam database...	0.54	0.46	0.64	61	70781	39	3	31	5	71
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.61	0.83	33	6863	7	1	6	0	21
3J0L_7	-	-0.01	0.00	0.00	0	1213	12	0	12	0	17
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_2	-	0.25	0.24	0.26	8	6185	25	2	21	2	25
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_a	-	0.39	0.31	0.50	5	1118	5	2	3	0	11
3J0L_1	-	0.76	0.63	0.92	12	1212	2	0	1	1	7
3J0L_h	-	0.81	0.65	1.00	28	6077	2	0	0	2	15
3J16_L	tRNA links to Rfam database...	0.29	0.23	0.37	7	2756	12	0	12	0	23
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.49	0.44	0.56	276	1116272	221	10	207	4	357
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...	0.73	0.70	0.76	16	2905	5	0	5	0	7
3J2C_M	-	0.38	0.31	0.47	64	106354	76	10	63	3	143
3J2C_O	-	0.63	0.51	0.78	32	10255	10	0	9	1	31
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.53	0.74	28	7837	12	0	10	2	25
3J3D_C	tRNA links to Rfam database...	0.47	0.43	0.52	12	2752	11	1	10	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...	0.07	0.06	0.08	2	7478	32	2	21	9	31
3J3F_8	5_8S_rRNA links to Rfam database...	0.32	0.31	0.33	11	12213	36	3	19	14	25
3J3F_7	5S_rRNA links to Rfam database...	0.79	0.68	0.92	34	7223	4	0	3	1	16
3J3V_B	5S_rRNA links to Rfam database...	0.50	0.40	0.62	23	6984	14	1	13	0	34
3JYV_7	tRNA links to Rfam database...	0.41	0.31	0.56	10	2832	8	0	8	0	22
3JYX_3	5S_rRNA links to Rfam database...	0.64	0.63	0.65	17	6302	19	1	8	10	10
3JYX_4	5_8S_rRNA links to Rfam database...	0.31	0.30	0.31	10	12214	34	4	18	12	23
3KIY_A	-	0.54	0.45	0.65	553	4053271	314	23	281	10	688
3KTW_C	-	0.54	0.47	0.65	20	4529	12	2	9	1	23
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NDB_M	-	0.78	0.69	0.89	42	9133	6	0	5	1	19
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3NMU_E	-	-0.01	0.00	0.00	0	553	10	1	7	2	6
3NPB_A	SAM links to Rfam database...	0.71	0.61	0.82	28	6987	9	0	6	3	18
3O58_3	5_8S_rRNA links to Rfam database...	0.35	0.34	0.35	12	12369	35	2	20	13	23
3O58_2	5S_rRNA links to Rfam database...	0.75	0.76	0.74	29	7221	11	3	7	1	9
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...	0.76	0.63	0.94	45	12832	5	0	3	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...	0.58	0.48	0.71	20	3888	8	1	7	0	22
3SIU_F	-	0.85	0.73	1.00	8	370	0	0	0	0	3
3SN2_B	IRE_II links to Rfam database...	1.00	1.00	1.00	12	394	0	0	0	0	0
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	-	0.45	0.35	0.59	13	3138	9	1	8	0	24
3UZL_B	tRNA links to Rfam database...	0.77	0.62	0.96	23	3546	1	0	1	0	14
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...	0.88	0.78	1.00	31	4722	1	0	0	1	9
3ZEX_H	-	0.19	0.18	0.19	7	9009	29	5	24	0	31
3ZEX_B	-	0.30	0.26	0.35	147	1071957	289	29	247	13	411
3ZEX_D	5S_rRNA links to Rfam database...	0.69	0.61	0.79	30	6983	8	1	7	0	19
3ZEX_E	-	0.00	0.00	0.00	0	21893	54	2	50	2	77
3ZEX_G	-	0.77	0.66	0.91	49	16417	11	0	5	6	25
3ZEX_C	5_8S_rRNA links to Rfam database...	0.41	0.27	0.64	14	14174	16	2	6	8	38
3ZEX_F	-	0.00	0.00	0.00	0	2617	11	2	9	0	12
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	23	1	20	2	18
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	0	6	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11746	41	4	26	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	-	0.38	0.30	0.50	3	522	3	0	3	0	7
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...	0.31	0.26	0.38	5	1313	8	1	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...	0.30	0.22	0.41	7	3469	10	1	9	0	25
4FRN_A	AdoCbl-variant links to Rfam database...	0.45	0.36	0.57	13	5128	10	2	8	0	23
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	-	0.29	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 MaxExpect - scored lower in this pairwise comparison

1. Total counts & total scores for MaxExpect

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