CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAsubopt		RDfolder
MCC	0.691	>	0.596
Average MCC ± 95% Confidence Intervals	0.711 ± 0.063	>	0.623 ± 0.071
Sensitivity	0.614	>	0.495
Positive Predictive Value	0.784	>	0.727
Total TP	1059	>	853
Total TN	130164	<	130341
Total FP	342	<	352
Total FP CONTRA	34	<	36
Total FP INCONS	257	<	284
Total FP COMP	51	>	32
Total FN	665	<	871
P-value	3.56938820447e-08

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Performance plots

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Performance of RNAsubopt - scored higher in this pairwise comparison

1. Total counts & total scores for RNAsubopt

Total Base Pair Counts
Total TP	1059
Total TN	130164
Total FP	342
Total FP CONTRA	34
Total FP INCONS	257
Total FP COMP	51
Total FN	665

Total Scores
MCC	0.691
Average MCC ± 95% Confidence Intervals	0.711 ± 0.063
Sensitivity	0.614
Positive Predictive Value	0.784
Nr of predictions	92

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2. Individual counts for RNAsubopt [ 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	396	0	0	0	0	1
2K63_A	-	0.89	0.80	1.00	8	398	0	0	0	0	2
2K66_A	-	0.95	0.90	1.00	9	222	0	0	0	0	1
2KD8_A	-	0.88	0.78	1.00	7	224	0	0	0	0	2
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2KE6_A	K10_TLS links to Rfam database...	0.86	0.84	0.89	16	1110	3	0	2	1	3
2KEZ_A	-	0.89	0.80	1.00	8	268	0	0	0	0	2
2KFC_A	-	-0.02	0.00	0.00	0	623	7	0	7	0	20
2KGP_A	-	1.00	1.00	1.00	9	291	0	0	0	0	0
2KMJ_A	-	1.00	1.00	1.00	11	367	0	0	0	0	0
2KPV_A	-	0.96	0.92	1.00	12	549	0	0	0	0	1
2KU0_A	-	0.83	0.69	1.00	11	692	0	0	0	0	5
2KUR_A	K10_TLS links to Rfam database...	0.85	0.81	0.89	17	1109	2	0	2	0	4
2KUU_A	K10_TLS links to Rfam database...	0.82	0.76	0.89	16	1110	3	0	2	1	5
2KUV_A	K10_TLS links to Rfam database...	0.83	0.77	0.89	17	1109	2	0	2	0	5
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...	0.91	0.83	1.00	15	846	0	0	0	0	3
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...	0.94	0.88	1.00	22	2123	0	0	0	0	3
2L1F_A	Gammaretro_CES links to Rfam database...	0.93	0.88	1.00	21	2059	0	0	0	0	3
2L2K_A	-	0.94	0.89	1.00	17	844	0	0	0	0	2
2L3C_B	-	0.87	0.76	1.00	13	548	0	0	0	0	4
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
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2RP0_A	-	0.64	0.42	1.00	5	346	0	0	0	0	7
2RPT_A	-	1.00	1.00	1.00	7	183	0	0	0	0	0
2RRC_A	-	0.83	0.70	1.00	7	224	0	0	0	0	3
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	12	5	3	4	7
2WW9_D	-	0.15	0.12	0.21	3	1939	11	4	7	0	23
2WW9_F	-	0.59	0.60	0.60	6	290	4	0	4	0	4
2WW9_E	-	-0.01	0.00	0.00	0	556	5	0	5	0	14
2WWQ_V	tRNA links to Rfam database...	0.76	0.68	0.86	19	2904	5	0	3	2	9
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.51	0.50	0.53	10	4541	23	0	9	14	10
2XQD_Y	tRNA links to Rfam database...	0.75	0.67	0.86	18	2829	3	0	3	0	9
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	-	-0.01	0.00	0.00	0	1525	15	3	12	0	12
2YIE_X	-	0.82	0.67	1.00	8	1370	3	0	0	3	4
2ZY6_A	-	0.58	0.58	0.58	7	691	5	1	4	0	5
2ZZM_B	tRNA links to Rfam database...	0.23	0.22	0.26	7	3459	20	2	18	0	25
2ZZN_D	tRNA links to Rfam database...	0.48	0.44	0.52	12	2462	11	1	10	0	15
3A2K_C	tRNA links to Rfam database...	0.42	0.39	0.46	11	2902	13	2	11	0	17
3A3A_A	tRNA-Sec links to Rfam database...	0.87	0.76	1.00	28	3627	0	0	0	0	9
3ADB_C	-	0.92	0.84	1.00	32	4154	0	0	0	0	6
3AKZ_H	tRNA links to Rfam database...	0.39	0.36	0.43	10	2678	13	2	11	0	18
3AM1_B	-	0.91	0.83	1.00	29	3211	0	0	0	0	6
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3DW4_A	-	-0.02	0.00	0.00	0	345	6	0	6	0	10
3GCA_A	-	0.54	0.29	1.00	5	523	0	0	0	0	12
3GX2_A	SAM links to Rfam database...	0.44	0.38	0.54	15	4343	14	1	12	1	25
3HAY_E	-	0.91	0.83	1.00	15	2263	3	0	0	3	3
3HJW_D	-	0.91	0.83	1.00	15	1638	2	0	0	2	3
3IAB_R	-	0.92	0.86	1.00	12	1023	0	0	0	0	2
3ID5_D	-	0.40	0.33	0.50	3	490	5	0	3	2	6
3IVN_B	Purine links to Rfam database...	0.76	0.58	1.00	18	2328	0	0	0	0	13
3IWN_A	c-di-GMP-I links to Rfam database...	0.63	0.58	0.70	19	4251	9	0	8	1	14
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_a	-	0.35	0.31	0.42	5	1116	7	1	6	0	11
3J0L_1	-	0.76	0.63	0.92	12	1212	2	0	1	1	7
3J0L_7	-	-0.01	0.00	0.00	0	1213	12	0	12	0	17
3J0L_g	-	-0.01	0.00	0.00	0	460	5	1	4	0	4
3J16_L	tRNA links to Rfam database...	0.41	0.37	0.48	11	2752	12	1	11	0	19
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2829	21	0	21	0	32
3KTW_C	-	0.75	0.65	0.88	28	4528	5	2	2	1	15
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NKB_B	-	0.57	0.50	0.65	13	1996	7	0	7	0	13
3NMU_E	-	0.54	0.50	0.60	3	556	5	0	2	3	3
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
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...	0.61	0.50	0.75	21	3888	7	1	6	0	21
3SIU_F	-	0.85	0.73	1.00	8	370	0	0	0	0	3
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
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.52	0.43	0.64	18	4343	11	2	8	1	24
4ENB_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1262	2	1	1	0	8
4ENC_A	crcB links to Rfam database...	0.32	0.26	0.42	5	1314	7	0	7	0	14

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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	853
Total TN	130341
Total FP	352
Total FP CONTRA	36
Total FP INCONS	284
Total FP COMP	32
Total FN	871

Total Scores
MCC	0.596
Average MCC ± 95% Confidence Intervals	0.623 ± 0.071
Sensitivity	0.495
Positive Predictive Value	0.727
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	399	0	0	0	0	4
2K63_A	-	0.89	0.80	1.00	8	398	0	0	0	0	2
2K66_A	-	0.89	0.80	1.00	8	223	0	0	0	0	2
2KD8_A	-	0.94	0.89	1.00	8	223	0	0	0	0	1
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2KE6_A	K10_TLS links to Rfam database...	0.89	0.79	1.00	15	1113	1	0	0	1	4
2KEZ_A	-	0.89	0.80	1.00	8	268	0	0	0	0	2
2KFC_A	-	0.49	0.25	1.00	5	625	0	0	0	0	15
2KGP_A	-	1.00	1.00	1.00	9	291	0	0	0	0	0
2KMJ_A	-	1.00	1.00	1.00	11	367	0	0	0	0	0
2KPV_A	-	0.96	0.92	1.00	12	549	0	0	0	0	1
2KU0_A	-	-0.01	0.00	0.00	0	696	7	0	7	0	16
2KUR_A	K10_TLS links to Rfam database...	0.87	0.76	1.00	16	1112	0	0	0	0	5
2KUU_A	K10_TLS links to Rfam database...	0.84	0.71	1.00	15	1113	1	0	0	1	6
2KUV_A	K10_TLS links to Rfam database...	0.85	0.73	1.00	16	1112	0	0	0	0	6
2KUW_A	K10_TLS links to Rfam database...	0.87	0.76	1.00	16	1112	0	0	0	0	5
2KX8_A	7SK links to Rfam database...	0.88	0.78	1.00	14	847	0	0	0	0	4
2KXM_A	-	0.70	0.50	1.00	5	346	0	0	0	0	5
2KZL_A	-	0.78	0.74	0.82	14	1468	3	1	2	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...	-0.01	0.00	0.00	0	2067	13	2	11	0	24
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	-	0.46	0.26	0.83	5	624	1	0	1	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	1526	14	2	12	0	20
2LDL_A	-	0.90	0.82	1.00	9	342	0	0	0	0	2
2LDT_A	-	0.68	0.47	1.00	7	458	0	0	0	0	8
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2RP0_A	-	0.64	0.42	1.00	5	346	0	0	0	0	7
2RPT_A	-	-0.03	0.00	0.00	0	186	4	1	3	0	7
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_F	-	0.71	0.60	0.86	6	293	1	0	1	0	4
2WW9_E	-	-0.01	0.00	0.00	0	556	5	0	5	0	14
2WWQ_V	tRNA links to Rfam database...	0.64	0.50	0.82	14	2909	4	0	3	1	14
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4538	22	5	17	0	20
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2Y8W_B	-	1.00	1.00	1.00	6	184	1	0	0	1	0
2Y9C_V	-	0.57	0.50	0.67	12	2260	7	1	5	1	12
2YIE_Z	-	0.43	0.42	0.45	5	1529	6	3	3	0	7
2YIE_X	-	0.38	0.33	0.44	4	1369	5	1	4	0	8
2ZY6_A	-	0.58	0.58	0.58	7	691	5	1	4	0	5
2ZZM_B	tRNA links to Rfam database...	0.10	0.09	0.13	3	3462	21	1	20	0	29
2ZZN_D	tRNA links to Rfam database...	0.84	0.78	0.91	21	2462	2	0	2	0	6
3A2K_C	tRNA links to Rfam database...	0.86	0.75	1.00	21	2905	0	0	0	0	7
3A3A_A	tRNA-Sec links to Rfam database...	0.53	0.41	0.71	15	3634	6	0	6	0	22
3ADB_C	-	0.46	0.39	0.54	15	4158	13	0	13	0	23
3AKZ_H	tRNA links to Rfam database...	0.48	0.43	0.55	12	2679	11	1	9	1	16
3AM1_B	-	0.47	0.43	0.54	15	3212	13	1	12	0	20
3AMU_B	tRNA links to Rfam database...	0.18	0.15	0.22	4	2985	16	2	12	2	23
3DW4_A	-	-0.02	0.00	0.00	0	347	4	0	4	0	10
3GCA_A	-	0.54	0.29	1.00	5	523	0	0	0	0	12
3GX2_A	SAM links to Rfam database...	0.50	0.40	0.64	16	4346	10	1	8	1	24
3HAY_E	-	0.91	0.83	1.00	15	2263	6	0	0	6	3
3HJW_D	-	0.85	0.78	0.93	14	1638	3	0	1	2	4
3IAB_R	-	0.86	0.86	0.86	12	1021	4	1	1	2	2
3ID5_D	-	-0.01	0.00	0.00	0	490	6	3	3	0	9
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...	0.00	0.00	0.00	0	4268	10	0	10	0	33
3J0L_8	-	0.86	0.75	1.00	6	184	0	0	0	0	2
3J0L_a	-	-0.01	0.00	0.00	0	1124	4	1	3	0	16
3J0L_1	-	0.65	0.47	0.90	9	1215	2	0	1	1	10
3J0L_7	-	-0.01	0.00	0.00	0	1220	5	0	5	0	17
3J0L_g	-	-0.01	0.00	0.00	0	462	3	1	2	0	4
3J16_L	tRNA links to Rfam database...	0.22	0.17	0.31	5	2759	11	0	11	0	25
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2830	20	0	20	0	32
3KTW_C	-	0.08	0.07	0.12	3	4535	23	0	22	1	40
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NKB_B	-	0.37	0.31	0.47	8	1999	9	0	9	0	18
3NMU_E	-	0.41	0.17	1.00	1	560	3	0	0	3	5
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	-	0.91	0.83	1.00	10	731	0	0	0	0	2
3R4F_A	-	0.76	0.68	0.85	17	2125	3	1	2	0	8
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...	0.30	0.17	0.54	7	3903	6	0	6	0	35
3SIU_F	-	0.73	0.55	1.00	6	372	0	0	0	0	5
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	0	0	0	0	1
3TS0_U	-	0.91	0.83	1.00	5	248	0	0	0	0	1
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENB_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1265	4	0	4	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	0	4	0	13

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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 RNAsubopt - scored higher in this pairwise comparison

1. Total counts & total scores for RNAsubopt

2. Individual counts for RNAsubopt [ 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 ]