CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Fold		Pknots
MCC	0.818	>	0.754
Average MCC ± 95% Confidence Intervals	0.812 ± 0.067	>	0.778 ± 0.069
Sensitivity	0.826	>	0.770
Positive Predictive Value	0.817	>	0.747
Total TP	1141	>	1064
Total TN	73268	>	73240
Total FP	410	<	490
Total FP CONTRA	60	<	94
Total FP INCONS	196	<	267
Total FP COMP	154	>	129
Total FN	241	<	318
P-value	3.56938820447e-08

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Performance plots

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

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Performance of Fold - scored higher in this pairwise comparison

1. Total counts & total scores for Fold

Total Base Pair Counts
Total TP	1141
Total TN	73268
Total FP	410
Total FP CONTRA	60
Total FP INCONS	196
Total FP COMP	154
Total FN	241

Total Scores
MCC	0.818
Average MCC ± 95% Confidence Intervals	0.812 ± 0.067
Sensitivity	0.826
Positive Predictive Value	0.817
Nr of predictions	80

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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_X	-	0.39	0.43	0.38	3	536	8	1	4	3	4
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
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
3IZF_C	5S_rRNA links to Rfam database...	0.87	0.89	0.86	31	2604	8	0	5	3	4
3J0L_2	-	0.30	0.31	0.31	8	2224	25	2	16	7	18
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
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

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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	1064
Total TN	73240
Total FP	490
Total FP CONTRA	94
Total FP INCONS	267
Total FP COMP	129
Total FN	318

Total Scores
MCC	0.754
Average MCC ± 95% Confidence Intervals	0.778 ± 0.069
Sensitivity	0.770
Positive Predictive Value	0.747
Nr of predictions	80

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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
2KPV_A	-	0.96	0.92	1.00	12	201	0	0	0	0	1
2KRL_A	-	0.79	0.83	0.76	19	1999	13	5	1	7	4
2KU0_A	-	-0.04	0.00	0.00	0	282	10	0	10	0	12
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	-	-0.04	0.00	0.00	0	144	5	0	5	0	8
2KZL_A	-	0.66	0.69	0.64	9	506	6	2	3	1	4
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	-	0.96	0.93	1.00	13	226	0	0	0	0	1
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	1	0	1	0	2
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.83	0.83	0.83	15	510	3	2	1	0	3
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	-	0.48	0.55	0.43	16	2403	23	9	12	2	13
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	0.38	0.27	0.60	3	202	3	0	2	1	8
2RRC_A	-	0.92	0.86	1.00	6	69	0	0	0	0	1
2WWQ_V	tRNA links to Rfam database...	0.29	0.32	0.29	6	1183	16	3	12	1	13
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.21	0.27	0.17	3	1817	33	3	12	18	8
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...	0.32	0.34	0.32	12	2008	26	1	24	1	23
2Y8W_B	-	1.00	1.00	1.00	6	82	1	0	0	1	0
2Y9C_V	-	0.70	0.67	0.75	12	890	6	0	4	2	6
2YIE_X	-	0.53	0.57	0.50	4	536	6	1	3	2	3
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
3ADB_C	-	0.98	0.97	1.00	32	1787	0	0	0	0	1
3AKZ_H	tRNA links to Rfam database...	1.00	1.00	1.00	20	1107	2	0	0	2	0
3AM1_B	-	1.00	1.00	1.00	29	1437	0	0	0	0	0
3AMU_B	tRNA links to Rfam database...	1.00	1.00	1.00	19	1138	3	0	0	3	0
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	9	0	5	4	3
3J0L_2	-	0.44	0.46	0.43	12	2222	23	1	15	7	14
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.35	0.36	0.36	4	400	8	3	4	1	7
3J0L_1	-	0.73	0.62	0.89	8	475	3	0	1	2	5
3J0L_h	-	0.67	0.66	0.70	21	2110	11	4	5	2	11
3J0L_7	-	0.38	0.50	0.31	5	503	12	3	8	1	5
3J0L_g	-	-0.02	0.00	0.00	0	171	5	3	2	0	2
3J16_L	tRNA links to Rfam database...	0.41	0.43	0.41	9	1137	13	1	12	0	12
3NDB_M	-	0.92	0.93	0.91	41	3669	8	3	1	4	3
3NKB_B	-	0.64	0.68	0.62	13	714	8	0	8	0	6
3NMU_E	-	1.00	1.00	1.00	3	213	5	0	0	5	0
3NPB_A	SAM links to Rfam database...	0.84	0.81	0.88	30	2244	9	0	4	5	7
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.45	0.24	10	4722	39	18	14	7	12
3O58_2	5S_rRNA links to Rfam database...	0.93	0.90	0.97	28	2725	3	0	1	2	3
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...	0.64	0.64	0.65	32	4791	19	4	13	2	18
3R4F_A	-	1.00	1.00	1.00	22	884	1	0	0	1	0
3R9X_C	-	0.87	0.88	0.88	7	221	5	0	1	4	1
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	0	1	0	3
3SD1_A	THF links to Rfam database...	0.78	0.76	0.81	22	1506	5	1	4	0	7
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	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	-	0.33	0.36	0.32	8	1251	17	4	13	0	14
3UZL_B	tRNA links to Rfam database...	1.00	1.00	1.00	16	1277	7	0	0	7	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...	0.33	0.40	0.29	8	4488	36	9	11	16	12
4A1C_3	5S_rRNA links to Rfam database...	0.28	0.30	0.28	11	2723	30	4	25	1	26
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.19	0.21	0.21	6	1409	23	3	19	1	23
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	2	0	0	2	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0

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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 Pknots - scored lower in this pairwise comparison

1. Total counts & total scores for Pknots

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