CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Afold		RNAfold
MCC	0.564	>	0.562
Average MCC ± 95% Confidence Intervals	0.741 ± 0.065	<	0.765 ± 0.062
Sensitivity	0.605	>	0.603
Positive Predictive Value	0.526	>	0.524
Total TP	2534	>	2528
Total TN	5463609	>	5463596
Total FP	2903	<	2904
Total FP CONTRA	694	<	700
Total FP INCONS	1585	<	1598
Total FP COMP	624	>	606
Total FN	1657	<	1663
P-value	5.84585956207e-05

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Performance plots

Comparison of performance of Afold and RNAfold. 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 Afold and RNAfold).
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 Afold and RNAfold).
Comparison of average Matthews Correlation Coefficients (MCCs) for Afold and RNAfold. 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 Afold and RNAfold).

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Performance of Afold - scored higher in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP	2534
Total TN	5463609
Total FP	2903
Total FP CONTRA	694
Total FP INCONS	1585
Total FP COMP	624
Total FN	1657

Total Scores
MCC	0.564
Average MCC ± 95% Confidence Intervals	0.741 ± 0.065
Sensitivity	0.605
Positive Predictive Value	0.526
Nr of predictions	105

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2. Individual counts for Afold [ 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	175	0	0	0	0	0
2K63_A	-	1.00	1.00	1.00	9	159	0	0	0	0	0
2K66_A	-	1.00	1.00	1.00	9	80	0	0	0	0	0
2KD8_A	-	1.00	1.00	1.00	9	99	0	0	0	0	0
2KDQ_B	mir-TAR links to Rfam database...	1.00	1.00	1.00	10	164	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	449	1	0	0	1	0
2KEZ_A	-	1.00	1.00	1.00	8	94	0	0	0	0	0
2KFC_A	-	-0.03	0.00	0.00	0	228	8	1	7	0	8
2KGP_A	-	1.00	1.00	1.00	9	112	1	0	0	1	0
2KMJ_A	-	1.00	1.00	1.00	11	157	0	0	0	0	0
2KPV_A	-	0.96	0.92	1.00	12	201	0	0	0	0	1
2KU0_A	-	1.00	1.00	1.00	12	280	0	0	0	0	0
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	1	0	0	1	0
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	1.00	0.96	24	766	1	0	1	0	0
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	1.00	0.96	23	739	1	0	1	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...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	6	0	5	1	7
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	-	1.00	1.00	1.00	29	2411	8	0	0	8	0
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	0.85	0.82	0.90	9	197	2	0	1	1	2
2RP0_A	-	0.76	0.71	0.83	5	110	1	0	1	0	2
2RPT_A	-	1.00	1.00	1.00	7	65	0	0	0	0	0
2WDL_A	-	0.52	0.54	0.50	426	1444477	465	78	341	46	362
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	14	0	0	14	0
2WW9_F	-	0.68	0.75	0.67	6	103	4	1	2	1	2
2WW9_E	-	0.79	0.80	0.80	4	167	1	0	1	0	1
2WW9_D	-	0.08	0.10	0.08	1	729	16	2	9	5	9
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.35	0.34	0.38	12	2013	21	1	19	1	23
2YIE_X	-	0.53	0.57	0.50	4	536	8	1	3	4	3
2YIE_Z	-	-0.02	0.00	0.00	0	587	16	6	9	1	8
2ZY6_A	-	0.63	0.78	0.54	7	263	6	3	3	0	2
2ZZM_B	tRNA links to Rfam database...	0.25	0.27	0.25	4	1342	20	3	9	8	11
2ZZN_D	tRNA links to Rfam database...	0.91	0.91	0.91	20	962	3	2	0	1	2
3A2K_C	tRNA links to Rfam database...	0.46	0.50	0.44	11	1083	14	3	11	0	11
3A3A_A	tRNA-Sec links to Rfam database...	0.93	0.87	1.00	26	1474	0	0	0	0	4
3ADB_C	-	0.85	0.85	0.85	28	1786	6	0	5	1	5
3AKZ_H	tRNA links to Rfam database...	0.19	0.20	0.21	4	1108	17	4	11	2	16
3AM1_B	-	0.79	0.79	0.79	23	1437	6	0	6	0	6
3DW4_A	-	-0.04	0.00	0.00	0	135	7	1	4	2	6
3G4S_9	5S_rRNA links to Rfam database...	0.73	0.69	0.78	18	2713	13	2	3	8	8
3GCA_A	-	-0.04	0.00	0.00	0	151	9	1	6	2	7
3HAY_E	-	1.00	1.00	1.00	14	910	8	0	0	8	0
3HJW_D	-	0.97	1.00	0.94	16	592	3	0	1	2	0
3IAB_R	-	1.00	1.00	1.00	12	373	0	0	0	0	0
3ID5_D	-	0.59	0.60	0.60	3	224	6	0	2	4	2
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.67	0.68	0.68	19	1444	9	1	8	0	9
3IYQ_A	tmRNA links to Rfam database...	0.23	0.33	0.17	17	22339	97	47	37	13	34
3IZ4_A	tmRNA links to Rfam database...	0.52	0.57	0.48	54	25423	63	27	32	4	41
3IZF_C	5S_rRNA links to Rfam database...	0.83	0.86	0.81	30	2603	11	0	7	4	5
3J0L_1	-	0.83	0.77	0.91	10	473	5	0	1	4	3
3J0L_7	-	-0.02	0.00	0.00	0	504	15	1	14	0	10
3J0L_h	-	0.87	0.81	0.93	26	2112	5	1	1	3	6
3J2C_O	-	0.70	0.68	0.72	28	3948	18	3	8	7	13
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1088	23	4	19	0	20
3JYX_3	5S_rRNA links to Rfam database...	0.64	0.67	0.63	10	2362	29	0	6	23	5
3JYX_4	5_8S_rRNA links to Rfam database...	0.61	0.83	0.45	10	4734	35	10	2	23	2
3JYX_5	-	0.34	0.44	0.27	210	1968232	793	260	300	233	271
3KIY_A	-	0.53	0.55	0.51	430	1485031	475	81	338	56	356
3KTW_C	-	0.94	0.96	0.92	24	1754	10	0	2	8	1
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NDB_M	-	1.00	1.00	1.00	44	3670	4	0	0	4	0
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NMU_E	-	-0.02	0.00	0.00	0	208	10	5	3	2	3
3NPB_A	SAM links to Rfam database...	0.82	0.73	0.93	27	2249	6	0	2	4	10
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	38	6	15	17	11
3O58_2	5S_rRNA links to Rfam database...	0.80	0.81	0.81	25	2723	14	0	6	8	6
3OVS_D	-	0.82	0.83	0.83	10	204	2	0	2	0	2
3P22_G	-	0.91	0.91	0.91	10	301	1	0	1	0	1
3R4F_A	-	1.00	1.00	1.00	22	884	1	0	0	1	0
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SIU_F	-	1.00	1.00	1.00	8	137	0	0	0	0	0
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3VJR_D	-	1.00	1.00	1.00	12	239	1	0	0	1	0
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.55	0.56	18	1957	15	4	10	1	15
3ZEX_F	-	-0.01	0.00	0.00	0	908	12	2	4	6	4
3ZEX_E	-	-0.01	0.00	0.00	0	8251	55	17	36	2	34
3ZEX_D	5S_rRNA links to Rfam database...	0.82	0.77	0.87	27	2765	8	0	4	4	8
3ZEX_B	-	0.34	0.38	0.31	132	420926	337	77	217	43	214
3ZEX_H	-	0.25	0.37	0.18	7	3586	33	20	12	1	12
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	43	11	17	15	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4ATO_G	-	0.38	0.43	0.38	3	212	6	5	0	1	4
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	4
4FNJ_A	-	0.86	0.83	0.91	10	239	1	0	1	0	2
4HXH_A	-	1.00	1.00	1.00	6	89	1	0	0	1	0

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Performance of RNAfold - scored lower in this pairwise comparison

1. Total counts & total scores for RNAfold

Total Base Pair Counts
Total TP	2528
Total TN	5463596
Total FP	2904
Total FP CONTRA	700
Total FP INCONS	1598
Total FP COMP	606
Total FN	1663

Total Scores
MCC	0.562
Average MCC ± 95% Confidence Intervals	0.765 ± 0.062
Sensitivity	0.603
Positive Predictive Value	0.524
Nr of predictions	105

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2. Individual counts for RNAfold [ 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	175	0	0	0	0	0
2K63_A	-	1.00	1.00	1.00	9	159	0	0	0	0	0
2K66_A	-	1.00	1.00	1.00	9	80	0	0	0	0	0
2KD8_A	-	1.00	1.00	1.00	9	99	0	0	0	0	0
2KDQ_B	mir-TAR links to Rfam database...	1.00	1.00	1.00	10	164	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	449	1	0	0	1	0
2KEZ_A	-	1.00	1.00	1.00	8	94	0	0	0	0	0
2KFC_A	-	-0.03	0.00	0.00	0	229	7	1	6	0	8
2KGP_A	-	1.00	1.00	1.00	9	112	1	0	0	1	0
2KMJ_A	-	1.00	1.00	1.00	11	157	0	0	0	0	0
2KPV_A	-	0.96	0.92	1.00	12	201	0	0	0	0	1
2KU0_A	-	1.00	1.00	1.00	12	280	0	0	0	0	0
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	1	0	0	1	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...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	0	5	0	7
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	-	1.00	1.00	1.00	29	2411	8	0	0	8	0
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	0.95	0.91	1.00	10	197	1	0	0	1	1
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2RPT_A	-	1.00	1.00	1.00	7	65	0	0	0	0	0
2WDL_A	-	0.49	0.52	0.47	408	1444460	493	86	368	39	380
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	14	0	0	14	0
2WW9_F	-	0.68	0.75	0.67	6	103	4	1	2	1	2
2WW9_E	-	0.89	0.80	1.00	4	168	0	0	0	0	1
2WW9_D	-	0.08	0.10	0.08	1	729	15	2	9	4	9
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.35	0.34	0.38	12	2013	21	1	19	1	23
2YIE_X	-	0.33	0.43	0.27	3	533	11	3	5	3	4
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
2ZY6_A	-	0.66	0.78	0.58	7	264	5	3	2	0	2
2ZZM_B	tRNA links to Rfam database...	0.25	0.27	0.25	4	1342	20	3	9	8	11
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	3	2	0	1	1
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3ADB_C	-	0.35	0.36	0.36	12	1786	22	1	20	1	21
3AKZ_H	tRNA links to Rfam database...	0.48	0.50	0.48	10	1106	13	4	7	2	10
3AM1_B	-	0.74	0.76	0.73	22	1436	8	3	5	0	7
3DW4_A	-	-0.03	0.00	0.00	0	136	6	1	3	2	6
3G4S_9	5S_rRNA links to Rfam database...	0.78	0.77	0.80	20	2711	12	2	3	7	6
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3HAY_E	-	1.00	1.00	1.00	14	910	7	0	0	7	0
3HJW_D	-	1.00	1.00	1.00	16	593	2	0	0	2	0
3IAB_R	-	1.00	1.00	1.00	12	373	0	0	0	0	0
3ID5_D	-	0.59	0.60	0.60	3	224	5	0	2	3	2
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.69	0.68	0.70	19	1445	9	1	7	1	9
3IYQ_A	tmRNA links to Rfam database...	0.24	0.33	0.17	17	22340	95	45	38	12	34
3IZ4_A	tmRNA links to Rfam database...	0.56	0.60	0.52	57	25426	57	26	27	4	38
3IZF_C	5S_rRNA links to Rfam database...	0.75	0.77	0.73	27	2603	15	0	10	5	8
3J0L_1	-	0.83	0.77	0.91	10	473	4	0	1	3	3
3J0L_7	-	-0.02	0.00	0.00	0	507	12	2	10	0	10
3J0L_h	-	0.87	0.81	0.93	26	2112	4	1	1	2	6
3J2C_O	-	0.76	0.76	0.78	31	3947	15	2	7	6	10
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1089	22	4	18	0	20
3JYX_3	5S_rRNA links to Rfam database...	0.77	0.80	0.75	12	2362	27	0	4	23	3
3JYX_4	5_8S_rRNA links to Rfam database...	0.61	0.83	0.45	10	4734	33	10	2	21	2
3JYX_5	-	0.36	0.46	0.29	220	1968243	783	251	288	244	261
3KIY_A	-	0.50	0.53	0.48	414	1485013	501	90	363	48	372
3KTW_C	-	0.96	0.96	0.96	24	1755	9	0	1	8	1
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NDB_M	-	0.93	0.93	0.93	41	3670	9	0	3	6	3
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NMU_E	-	1.00	1.00	1.00	3	213	5	0	0	5	0
3NPB_A	SAM links to Rfam database...	0.91	0.86	0.97	32	2245	5	1	0	4	5
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	35	6	15	14	11
3O58_2	5S_rRNA links to Rfam database...	0.72	0.74	0.70	23	2721	19	0	10	9	8
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
3R4F_A	-	1.00	1.00	1.00	22	884	1	0	0	1	0
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SIU_F	-	1.00	1.00	1.00	8	137	0	0	0	0	0
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.60	0.61	0.61	20	1956	14	4	9	1	13
3ZEX_F	-	-0.01	0.00	0.00	0	908	11	2	4	5	4
3ZEX_E	-	0.00	0.00	0.00	0	8255	54	17	32	5	34
3ZEX_D	5S_rRNA links to Rfam database...	0.88	0.83	0.94	29	2765	6	0	2	4	6
3ZEX_B	-	0.35	0.39	0.32	136	420925	333	77	214	42	210
3ZEX_H	-	0.25	0.37	0.18	7	3586	32	20	12	0	12
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4482	43	11	18	14	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4ATO_G	-	0.38	0.43	0.38	3	212	5	5	0	0	4
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4FNJ_A	-	0.91	0.83	1.00	10	240	0	0	0	0	2
4HXH_A	-	1.00	1.00	1.00	6	89	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 Afold - scored higher in this pairwise comparison

1. Total counts & total scores for Afold

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

Performance of RNAfold - scored lower in this pairwise comparison

1. Total counts & total scores for RNAfold

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