CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	UNAFold		RDfolder
MCC	0.827	>	0.682
Average MCC ± 95% Confidence Intervals	0.828 ± 0.056	>	0.691 ± 0.076
Sensitivity	0.822	>	0.643
Positive Predictive Value	0.841	>	0.739
Total TP	1078	>	843
Total TN	50000	<	50142
Total FP	319	<	362
Total FP CONTRA	59	<	72
Total FP INCONS	145	<	225
Total FP COMP	115	>	65
Total FN	233	<	468
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of UNAFold and RDfolder. 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 UNAFold and RDfolder).
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 UNAFold and RDfolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for UNAFold and RDfolder. 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 UNAFold and RDfolder).

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Performance of UNAFold - scored higher in this pairwise comparison

1. Total counts & total scores for UNAFold

Total Base Pair Counts
Total TP	1078
Total TN	50000
Total FP	319
Total FP CONTRA	59
Total FP INCONS	145
Total FP COMP	115
Total FN	233

Total Scores
MCC	0.827
Average MCC ± 95% Confidence Intervals	0.828 ± 0.056
Sensitivity	0.822
Positive Predictive Value	0.841
Nr of predictions	92

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2K5Z_A	-	0.95	0.91	1.00	10	176	0	0	0	0	1
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	-	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...	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
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	-	0.95	0.91	1.00	10	152	0	0	0	0	1
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
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
2RRC_A	-	0.83	0.71	1.00	5	70	0	0	0	0	2
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	14	0	0	14	0
2WW9_D	-	0.13	0.10	0.20	1	736	9	1	3	5	9
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
2WWQ_V	tRNA links to Rfam database...	1.00	1.00	1.00	19	1185	3	0	0	3	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.58	0.64	0.54	7	1822	23	0	6	17	4
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2Y8W_B	-	1.00	1.00	1.00	6	82	1	0	0	1	0
2Y9C_V	-	0.75	0.78	0.74	14	887	8	0	5	3	4
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
2YIE_X	-	0.53	0.57	0.50	4	536	6	1	3	2	3
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	2	2	0	0	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	-	0.86	0.85	0.88	28	1787	4	0	4	0	5
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
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3DW4_A	-	0.91	0.83	1.00	5	135	2	0	0	2	1
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.81	0.79	0.85	22	1423	5	2	2	1	6
3HAY_E	-	1.00	1.00	1.00	14	910	7	0	0	7	0
3HJW_D	-	0.97	0.94	1.00	15	594	2	0	0	2	1
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...	0.80	0.79	0.81	22	1445	6	1	4	1	6
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.55	0.64	0.50	7	397	8	5	2	1	4
3J0L_1	-	0.75	0.69	0.82	9	473	4	0	2	2	4
3J0L_7	-	0.66	0.70	0.64	7	508	5	2	2	1	3
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J16_L	tRNA links to Rfam database...	0.31	0.33	0.30	7	1136	16	3	13	0	14
3JYV_7	tRNA links to Rfam database...	0.24	0.25	0.25	5	1091	16	7	8	1	15
3KTW_C	-	1.00	1.00	1.00	25	1755	7	0	0	7	0
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
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
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
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...	0.77	0.76	0.79	22	1505	6	4	2	0	7
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
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
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...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.37	0.33	0.45	5	485	7	0	6	1	10

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Performance of RDfolder - scored lower in this pairwise comparison

1. Total counts & total scores for RDfolder

Total Base Pair Counts
Total TP	843
Total TN	50142
Total FP	362
Total FP CONTRA	72
Total FP INCONS	225
Total FP COMP	65
Total FN	468

Total Scores
MCC	0.682
Average MCC ± 95% Confidence Intervals	0.691 ± 0.076
Sensitivity	0.643
Positive Predictive Value	0.739
Nr of predictions	92

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2K5Z_A	-	0.79	0.64	1.00	7	179	0	0	0	0	4
2K63_A	-	0.94	0.89	1.00	8	160	0	0	0	0	1
2K66_A	-	0.94	0.89	1.00	8	81	0	0	0	0	1
2KD8_A	-	0.94	0.89	1.00	8	100	0	0	0	0	1
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...	0.91	0.83	1.00	15	452	1	0	0	1	3
2KEZ_A	-	1.00	1.00	1.00	8	94	0	0	0	0	0
2KFC_A	-	0.79	0.63	1.00	5	231	0	0	0	0	3
2KGP_A	-	1.00	1.00	1.00	9	112	0	0	0	0	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	-	-0.03	0.00	0.00	0	285	7	2	5	0	12
2KUR_A	K10_TLS links to Rfam database...	0.91	0.84	1.00	16	451	0	0	0	0	3
2KUU_A	K10_TLS links to Rfam database...	0.91	0.83	1.00	15	432	1	0	0	1	3
2KUV_A	K10_TLS links to Rfam database...	0.91	0.84	1.00	16	423	0	0	0	0	3
2KUW_A	K10_TLS links to Rfam database...	0.94	0.89	1.00	16	454	0	0	0	0	2
2KX8_A	7SK links to Rfam database...	0.93	0.88	1.00	14	357	0	0	0	0	2
2KXM_A	-	0.78	0.63	1.00	5	144	0	0	0	0	3
2KZL_A	-	1.00	1.00	1.00	13	507	4	0	0	4	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...	-0.02	0.00	0.00	0	750	13	2	11	0	23
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	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...	-0.03	0.00	0.00	0	514	14	3	11	0	18
2LDL_A	-	1.00	1.00	1.00	9	131	0	0	0	0	0
2LDT_A	-	0.79	0.64	1.00	7	155	0	0	0	0	4
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2RPT_A	-	-0.07	0.00	0.00	0	68	4	1	3	0	7
2RRC_A	-	0.83	0.71	1.00	5	70	0	0	0	0	2
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	13	0	0	13	0
2WW9_D	-	0.31	0.10	1.00	1	740	3	0	0	3	9
2WW9_F	-	0.86	0.75	1.00	6	106	1	0	0	1	2
2WW9_E	-	-0.03	0.00	0.00	0	168	5	0	4	1	5
2WWQ_V	tRNA links to Rfam database...	0.80	0.74	0.88	14	1188	4	0	2	2	5
2XKV_B	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	1813	22	10	12	0	11
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2Y8W_B	-	1.00	1.00	1.00	6	82	1	0	0	1	0
2Y9C_V	-	0.68	0.67	0.71	12	889	7	0	5	2	6
2YIE_Z	-	0.53	0.63	0.45	5	591	6	4	2	0	3
2YIE_X	-	0.57	0.57	0.57	4	537	5	0	3	2	3
2ZY6_A	-	0.66	0.78	0.58	7	264	5	3	2	0	2
2ZZM_B	tRNA links to Rfam database...	0.15	0.20	0.13	3	1334	21	7	14	0	12
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	2	2	0	0	1
3A2K_C	tRNA links to Rfam database...	0.98	0.95	1.00	21	1087	0	0	0	0	1
3A3A_A	tRNA-Sec links to Rfam database...	0.59	0.50	0.71	15	1479	6	0	6	0	15
3ADB_C	-	0.48	0.45	0.54	15	1791	13	1	12	0	18
3AKZ_H	tRNA links to Rfam database...	0.53	0.55	0.52	11	1106	12	1	9	2	9
3AM1_B	-	0.52	0.52	0.54	15	1438	13	4	9	0	14
3AMU_B	tRNA links to Rfam database...	0.20	0.21	0.22	4	1139	16	4	10	2	15
3DW4_A	-	-0.03	0.00	0.00	0	136	4	1	3	0	6
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.60	0.57	0.64	16	1424	10	2	7	1	12
3HAY_E	-	1.00	1.00	1.00	14	910	7	0	0	7	0
3HJW_D	-	0.90	0.88	0.93	14	594	3	0	1	2	2
3IAB_R	-	1.00	1.00	1.00	12	373	4	0	0	4	0
3ID5_D	-	-0.02	0.00	0.00	0	223	6	3	3	0	5
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...	-0.01	0.00	0.00	0	1462	10	1	9	0	28
3J0L_8	-	0.92	0.86	1.00	6	70	0	0	0	0	1
3J0L_a	-	-0.02	0.00	0.00	0	407	4	3	1	0	11
3J0L_1	-	0.73	0.62	0.89	8	475	3	0	1	2	5
3J0L_7	-	-0.01	0.00	0.00	0	514	5	1	4	0	10
3J0L_g	-	-0.01	0.00	0.00	0	173	3	2	1	0	2
3J16_L	tRNA links to Rfam database...	0.26	0.24	0.31	5	1143	11	0	11	0	16
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1091	20	4	16	0	20
3KTW_C	-	0.11	0.12	0.13	3	1757	23	3	17	3	22
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.43	0.42	0.47	8	718	9	2	7	0	11
3NMU_E	-	0.57	0.33	1.00	1	215	3	0	0	3	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	-	0.95	0.91	1.00	10	302	0	0	0	0	1
3R4F_A	-	0.78	0.73	0.84	16	887	4	2	1	1	6
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...	0.35	0.24	0.54	7	1520	6	1	5	0	22
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	0	0	0	0	0
3TS0_U	-	0.91	0.83	1.00	5	113	0	0	0	0	1
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ENB_A	crcB links to Rfam database...	0.48	0.40	0.60	6	462	4	0	4	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	0	4	0	9

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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 UNAFold - scored higher in this pairwise comparison

1. Total counts & total scores for UNAFold

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

Performance of RDfolder - scored lower in this pairwise comparison

1. Total counts & total scores for RDfolder

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