CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

Home

Methods

Datasets

Rankings

RNA 2D Atlas

Help

FAQ

Contact us

RSS feeds

Twitter

Overview

Metric	Fold		Contrafold
MCC	0.777	>	0.773
Average MCC ± 95% Confidence Intervals	0.802 ± 0.067	<	0.828 ± 0.056
Sensitivity	0.796	>	0.790
Positive Predictive Value	0.764	>	0.763
Total TP	1216	>	1207
Total TN	121050	<	121059
Total FP	552	>	548
Total FP CONTRA	116	<	126
Total FP INCONS	259	>	249
Total FP COMP	177	>	173
Total FN	312	<	321
P-value	0.000284355681826

^top

Performance plots

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

^top

Performance of Fold - scored higher in this pairwise comparison

1. Total counts & total scores for Fold

Total Base Pair Counts
Total TP	1216
Total TN	121050
Total FP	552
Total FP CONTRA	116
Total FP INCONS	259
Total FP COMP	177
Total FN	312

Total Scores
MCC	0.777
Average MCC ± 95% Confidence Intervals	0.802 ± 0.067
Sensitivity	0.796
Positive Predictive Value	0.764
Nr of predictions	82

^top

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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...	1.00	1.00	1.00	19	448	0	0	0	0	0
2KUU_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	429	1	0	0	1	0
2KUV_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	420	0	0	0	0	0
2KUW_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	452	1	0	0	1	0
2KX8_A	7SK links to Rfam database...	1.00	1.00	1.00	16	355	0	0	0	0	0
2KXM_A	-	0.93	0.88	1.00	7	142	0	0	0	0	1
2KZL_A	-	1.00	1.00	1.00	13	507	1	0	0	1	0
2L1F_B	Gammaretro_CES links to Rfam database...	0.91	0.92	0.92	22	767	2	0	2	0	2
2L1F_A	Gammaretro_CES links to Rfam database...	0.91	0.91	0.91	21	740	2	0	2	0	2
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...	-0.03	0.00	0.00	0	513	15	3	12	0	18
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
2LI4_A	-	1.00	1.00	1.00	14	175	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	-	0.90	0.90	0.90	26	2411	10	0	3	7	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
2RRC_A	-	0.83	0.71	1.00	5	70	0	0	0	0	2
2WWQ_V	tRNA links to Rfam database...	0.97	0.95	1.00	18	1186	3	0	0	3	1
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	26	0	6	20	3
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...	1.00	1.00	1.00	35	2010	1	0	0	1	0
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	-	0.39	0.43	0.38	3	536	8	1	4	3	4
3ADB_C	-	0.86	0.85	0.88	28	1787	4	0	4	0	5
3AKZ_H	tRNA links to Rfam database...	1.00	1.00	1.00	20	1107	2	0	0	2	0
3AM1_B	-	0.86	0.86	0.86	25	1437	4	0	4	0	4
3AMU_B	tRNA links to Rfam database...	0.73	0.79	0.68	15	1135	10	0	7	3	4
3IYQ_A	tmRNA links to Rfam database...	0.24	0.33	0.18	17	22345	95	40	38	17	34
3IZ4_A	tmRNA links to Rfam database...	0.60	0.61	0.59	58	25437	47	16	25	6	37
3IZF_C	5S_rRNA links to Rfam database...	0.87	0.89	0.86	31	2604	8	0	5	3	4
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.15	0.18	0.17	2	399	11	4	6	1	9
3J0L_1	-	0.83	0.77	0.91	10	473	4	0	1	3	3
3J0L_h	-	0.93	0.88	1.00	28	2112	2	0	0	2	4
3J0L_7	-	-0.02	0.00	0.00	0	507	12	2	10	0	10
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_2	-	0.30	0.31	0.31	8	2224	25	2	16	7	18
3J16_L	tRNA links to Rfam database...	0.76	0.76	0.76	16	1138	5	0	5	0	5
3NDB_M	-	1.00	1.00	1.00	44	3670	4	0	0	4	0
3NKB_B	-	0.41	0.42	0.42	8	716	11	4	7	0	11
3NMU_E	-	-0.02	0.00	0.00	0	207	11	6	3	2	3
3NPB_A	SAM links to Rfam database...	0.77	0.73	0.82	27	2245	11	0	6	5	10
3O58_3	5_8S_rRNA links to Rfam database...	0.39	0.50	0.31	11	4728	41	9	16	16	11
3O58_2	5S_rRNA links to Rfam database...	0.86	0.87	0.84	27	2722	12	0	5	7	4
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...	0.93	0.92	0.94	46	4791	5	1	2	2	4
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...	0.68	0.69	0.69	20	1504	9	4	5	0	9
3SIU_F	-	1.00	1.00	1.00	8	137	0	0	0	0	0
3SN2_B	IRE_II links to Rfam database...	1.00	1.00	1.00	12	142	0	0	0	0	0
3TRZ_Z	-	1.00	1.00	1.00	5	87	1	0	0	1	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	-	0.58	0.59	0.59	13	1254	9	2	7	0	9
3UZL_B	tRNA links to Rfam database...	1.00	1.00	1.00	16	1277	8	0	0	8	0
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4482	43	11	18	14	15
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.84	0.89	31	2728	7	0	4	3	6
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
4ENB_A	crcB links to Rfam database...	0.37	0.33	0.45	5	461	7	0	6	1	10
4ENC_A	crcB links to Rfam database...	0.36	0.33	0.42	5	484	8	0	7	1	10

^top

Performance of Contrafold - scored lower in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP	1207
Total TN	121059
Total FP	548
Total FP CONTRA	126
Total FP INCONS	249
Total FP COMP	173
Total FN	321

Total Scores
MCC	0.773
Average MCC ± 95% Confidence Intervals	0.828 ± 0.056
Sensitivity	0.790
Positive Predictive Value	0.763
Nr of predictions	82

^top

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
2KPV_A	-	1.00	1.00	1.00	13	200	0	0	0	0	0
2KRL_A	-	0.91	0.87	0.95	20	2003	9	1	0	8	3
2KU0_A	-	0.63	0.58	0.70	7	282	3	2	1	0	5
2KUR_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	448	0	0	0	0	0
2KUU_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	429	1	0	0	1	0
2KUV_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	420	0	0	0	0	0
2KUW_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	452	1	0	0	1	0
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	5	0	0	5	0
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	0	0	0	0	0
2L1F_A	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	23	740	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...	0.94	0.94	0.94	17	339	2	0	1	1	1
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	3	2	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
2LI4_A	-	1.00	1.00	1.00	14	175	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	-	0.88	0.90	0.87	26	2410	11	0	4	7	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
2RRC_A	-	1.00	1.00	1.00	7	68	0	0	0	0	0
2WWQ_V	tRNA links to Rfam database...	1.00	1.00	1.00	19	1185	4	0	0	4	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	27	0	6	21	3
2XQD_Y	tRNA links to Rfam database...	0.85	0.86	0.86	18	1108	4	0	3	1	3
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.10	0.11	0.12	4	2012	30	2	27	1	31
2Y8W_B	-	1.00	1.00	1.00	6	82	3	0	0	3	0
2Y9C_V	-	0.79	0.83	0.75	15	886	8	0	5	3	3
2YIE_Z	-	0.53	0.63	0.45	5	591	6	4	2	0	3
2YIE_X	-	1.00	1.00	1.00	7	537	4	0	0	4	0
3ADB_C	-	0.98	0.97	1.00	32	1787	0	0	0	0	1
3AKZ_H	tRNA links to Rfam database...	0.44	0.50	0.40	10	1102	18	6	9	3	10
3AM1_B	-	0.74	0.76	0.73	22	1436	8	3	5	0	7
3AMU_B	tRNA links to Rfam database...	0.75	0.79	0.71	15	1136	9	0	6	3	4
3IYQ_A	tmRNA links to Rfam database...	0.28	0.39	0.20	20	22341	95	44	35	16	31
3IZ4_A	tmRNA links to Rfam database...	0.57	0.58	0.57	55	25440	49	18	23	8	40
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	11	0	5	6	3
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.53	0.55	0.55	6	400	6	3	2	1	5
3J0L_1	-	0.83	0.77	0.91	10	473	3	0	1	2	3
3J0L_h	-	0.87	0.88	0.88	28	2108	6	0	4	2	4
3J0L_7	-	-0.02	0.00	0.00	0	512	7	1	6	0	10
3J0L_g	-	0.00	0.00	0.00	0	176	1	0	0	1	2
3J0L_2	-	0.28	0.31	0.28	8	2221	26	2	19	5	18
3J16_L	tRNA links to Rfam database...	0.55	0.57	0.55	12	1137	10	3	7	0	9
3NDB_M	-	0.98	0.98	0.98	43	3670	6	0	1	5	1
3NKB_B	-	0.63	0.68	0.59	13	713	9	0	9	0	6
3NMU_E	-	1.00	1.00	1.00	3	213	3	0	0	3	0
3NPB_A	SAM links to Rfam database...	0.86	0.84	0.89	31	2243	9	1	3	5	6
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.36	0.29	8	4736	21	7	13	1	14
3O58_2	5S_rRNA links to Rfam database...	0.92	0.94	0.91	29	2722	10	0	3	7	2
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	1	0	0	1	0
3PDR_A	ykoK links to Rfam database...	0.83	0.86	0.80	43	4786	13	5	6	2	7
3R4F_A	-	0.81	0.82	0.82	18	884	5	2	2	1	4
3R9X_C	-	1.00	1.00	1.00	8	221	2	0	0	2	0
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SD1_A	THF links to Rfam database...	0.68	0.69	0.69	20	1504	9	5	4	0	9
3SIU_F	-	0.87	0.88	0.88	7	137	1	0	1	0	1
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	1	0	0	1	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	-	0.81	0.77	0.85	17	1256	5	0	3	2	5
3UZL_B	tRNA links to Rfam database...	0.90	0.88	0.93	14	1278	8	0	1	7	2
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.25	0.19	5	4489	33	9	13	11	15
4A1C_3	5S_rRNA links to Rfam database...	0.81	0.81	0.81	30	2726	10	0	7	3	7
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.53	0.52	0.56	15	1410	13	3	9	1	14
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	1	0	0	1	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	1	0	0	1	4

^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 Fold - scored higher in this pairwise comparison

1. Total counts & total scores for Fold

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

Performance of Contrafold - scored lower in this pairwise comparison

1. Total counts & total scores for Contrafold

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