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		MCFold
MCC	0.777	>	0.678
Average MCC ± 95% Confidence Intervals	0.786 ± 0.059	>	0.702 ± 0.067
Sensitivity	0.787	>	0.717
Positive Predictive Value	0.775	>	0.653
Total TP	1347	>	1227
Total TN	89377	>	89234
Total FP	600	<	900
Total FP CONTRA	97	<	175
Total FP INCONS	293	<	478
Total FP COMP	210	<	247
Total FN	364	<	484
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of RNAsubopt and MCFold. 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 RNAsubopt and MCFold).
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 RNAsubopt and MCFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAsubopt and MCFold. 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 RNAsubopt and MCFold).

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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	1347
Total TN	89377
Total FP	600
Total FP CONTRA	97
Total FP INCONS	293
Total FP COMP	210
Total FN	364

Total Scores
MCC	0.777
Average MCC ± 95% Confidence Intervals	0.786 ± 0.059
Sensitivity	0.787
Positive Predictive Value	0.775
Nr of predictions	109

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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	176	0	0	0	0	1
2K63_A	-	0.94	0.89	1.00	8	160	0	0	0	0	1
2K66_A	-	1.00	1.00	1.00	9	80	0	0	0	0	0
2KD8_A	-	0.87	0.78	1.00	7	101	0	0	0	0	2
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...	0.88	0.89	0.89	16	449	3	0	2	1	2
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	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	-	0.96	0.92	1.00	11	281	0	0	0	0	1
2KUR_A	K10_TLS links to Rfam database...	0.89	0.89	0.89	17	448	2	0	2	0	2
2KUU_A	K10_TLS links to Rfam database...	0.88	0.89	0.89	16	429	3	0	2	1	2
2KUV_A	K10_TLS links to Rfam database...	0.89	0.89	0.89	17	420	2	0	2	0	2
2KUW_A	K10_TLS links to Rfam database...	0.94	0.94	0.94	17	452	2	0	1	1	1
2KX8_A	7SK links to Rfam database...	0.97	0.94	1.00	15	356	0	0	0	0	1
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_A	Gammaretro_CES links to Rfam database...	0.95	0.91	1.00	21	742	0	0	0	0	2
2L1F_B	Gammaretro_CES links to Rfam database...	0.96	0.92	1.00	22	769	0	0	0	0	2
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...	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	-	0.85	0.86	0.83	25	2410	14	0	5	9	4
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
2RRC_A	-	1.00	1.00	1.00	7	68	0	0	0	0	0
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	13	0	0	13	0
2WW9_F	-	0.52	0.63	0.50	5	102	5	1	4	0	3
2WW9_E	-	-0.03	0.00	0.00	0	168	5	0	4	1	5
2WW9_D	-	0.09	0.10	0.11	1	732	13	2	6	5	9
2WWQ_V	tRNA links to Rfam database...	1.00	1.00	1.00	19	1185	5	0	0	5	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	25	0	6	19	3
2XQD_Y	tRNA links to Rfam database...	0.83	0.81	0.85	17	1109	4	0	3	1	4
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.49	0.49	0.52	17	2012	17	1	15	1	18
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	-	1.00	1.00	1.00	7	537	4	0	0	4	0
2ZY6_A	-	0.66	0.78	0.58	7	264	5	3	2	0	2
2ZZN_D	tRNA links to Rfam database...	0.52	0.55	0.52	12	961	11	3	8	0	10
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
3AKZ_H	tRNA links to Rfam database...	0.43	0.45	0.43	9	1106	14	3	9	2	11
3AM1_B	-	1.00	1.00	1.00	29	1437	0	0	0	0	0
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3DW4_A	-	-0.03	0.00	0.00	0	136	6	1	3	2	6
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.53	0.54	0.54	15	1421	14	4	9	1	13
3HAY_E	-	1.00	1.00	1.00	14	910	4	0	0	4	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	-	0.54	0.60	0.50	3	223	5	1	2	2	2
3IVN_B	Purine links to Rfam database...	0.88	0.78	1.00	18	885	0	0	0	0	5
3IWN_A	c-di-GMP-I links to Rfam database...	0.69	0.68	0.70	19	1445	9	1	7	1	9
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	9	0	5	4	3
3J0L_g	-	-0.01	0.00	0.00	0	173	5	1	2	2	2
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	-	0.83	0.77	0.91	10	473	4	0	1	3	3
3J0L_h	-	0.87	0.81	0.93	26	2112	4	1	1	2	6
3J0L_7	-	-0.02	0.00	0.00	0	507	12	2	10	0	10
3J0L_2	-	0.28	0.31	0.28	8	2221	25	2	19	4	18
3J16_L	tRNA links to Rfam database...	0.49	0.52	0.48	11	1136	12	3	9	0	10
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1090	21	4	17	0	20
3JYX_4	5_8S_rRNA links to Rfam database...	0.34	0.58	0.21	7	4722	38	20	7	11	5
3JYX_3	5S_rRNA links to Rfam database...	0.77	0.80	0.75	12	2362	26	0	4	22	3
3KTW_C	-	1.00	1.00	1.00	25	1755	8	0	0	8	0
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	-	0.66	0.68	0.65	13	715	7	0	7	0	6
3NMU_E	-	1.00	1.00	1.00	3	213	5	0	0	5	0
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...	0.87	0.90	0.85	28	2721	13	0	5	8	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...	0.90	0.90	0.90	45	4790	7	2	3	2	5
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...	0.73	0.72	0.75	21	1505	7	4	3	0	8
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
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
4A1C_3	5S_rRNA links to Rfam database...	0.85	0.84	0.86	31	2727	8	0	5	3	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4481	43	13	17	13	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
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...	0.36	0.33	0.42	5	484	7	0	7	0	10

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Performance of MCFold - scored lower in this pairwise comparison

1. Total counts & total scores for MCFold

Total Base Pair Counts
Total TP	1227
Total TN	89234
Total FP	900
Total FP CONTRA	175
Total FP INCONS	478
Total FP COMP	247
Total FN	484

Total Scores
MCC	0.678
Average MCC ± 95% Confidence Intervals	0.702 ± 0.067
Sensitivity	0.717
Positive Predictive Value	0.653
Nr of predictions	109

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2. Individual counts for MCFold [ 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	4	0	0	4	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	1	0	0	1	0
2KDQ_B	mir-TAR links to Rfam database...	1.00	1.00	1.00	10	164	1	0	0	1	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	-	0.54	0.63	0.50	5	226	5	2	3	0	3
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	1	0	0	1	0
2KPV_A	-	1.00	1.00	1.00	13	200	0	0	0	0	0
2KU0_A	-	1.00	1.00	1.00	12	280	1	0	0	1	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	1	0	0	1	0
2KZL_A	-	1.00	1.00	1.00	13	507	5	0	0	5	0
2L1F_A	Gammaretro_CES links to Rfam database...	0.79	0.78	0.82	18	741	4	0	4	0	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.80	0.79	0.83	19	768	4	0	4	0	5
2L2K_A	-	1.00	1.00	1.00	17	332	1	0	0	1	0
2L3C_B	-	1.00	1.00	1.00	14	225	1	0	0	1	0
2L3E_A	-	1.00	1.00	1.00	12	228	2	0	0	2	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	-	-0.03	0.00	0.00	0	265	10	0	10	0	7
2LBS_A	-	1.00	1.00	1.00	14	193	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	0.44	0.44	0.47	8	511	10	0	9	1	10
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
2LHP_A	-	1.00	1.00	1.00	15	246	1	0	0	1	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	11	0	0	11	0
2LQZ_A	-	1.00	1.00	1.00	8	124	3	0	0	3	0
2LWK_A	-	1.00	1.00	1.00	11	196	2	0	0	2	0
2RP0_A	-	0.70	0.71	0.71	5	109	2	1	1	0	2
2RPT_A	-	1.00	1.00	1.00	7	65	0	0	0	0	0
2RRC_A	-	1.00	1.00	1.00	7	68	1	0	0	1	0
2WRQ_Y	tRNA links to Rfam database...	0.38	0.56	0.26	5	1133	21	8	6	7	4
2WW9_F	-	0.68	0.75	0.67	6	103	4	1	2	1	2
2WW9_E	-	-0.03	0.00	0.00	0	165	8	1	6	1	5
2WW9_D	-	-0.02	0.00	0.00	0	723	21	6	12	3	10
2WWQ_V	tRNA links to Rfam database...	0.19	0.21	0.19	4	1183	20	3	14	3	15
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.20	0.27	0.16	3	1816	30	4	12	14	8
2XQD_Y	tRNA links to Rfam database...	0.39	0.43	0.38	9	1105	18	2	13	3	12
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.23	0.26	0.24	9	2007	30	1	28	1	26
2Y8W_B	-	1.00	1.00	1.00	6	82	2	0	0	2	0
2Y9C_V	-	0.65	0.72	0.59	13	884	12	1	8	3	5
2YIE_Z	-	0.53	0.63	0.45	5	591	8	2	4	2	3
2YIE_X	-	-0.01	0.00	0.00	0	535	15	1	8	6	7
2ZY6_A	-	0.77	0.78	0.78	7	267	6	1	1	4	2
2ZZN_D	tRNA links to Rfam database...	0.69	0.73	0.67	16	960	11	1	7	3	6
3A2K_C	tRNA links to Rfam database...	0.49	0.55	0.46	12	1082	14	3	11	0	10
3A3A_A	tRNA-Sec links to Rfam database...	0.98	0.97	1.00	29	1471	0	0	0	0	1
3AKZ_H	tRNA links to Rfam database...	0.46	0.50	0.43	10	1104	16	5	8	3	10
3AM1_B	-	1.00	1.00	1.00	29	1437	1	0	0	1	0
3AMU_B	tRNA links to Rfam database...	0.50	0.58	0.44	11	1132	15	4	10	1	8
3DW4_A	-	1.00	1.00	1.00	6	134	3	0	0	3	0
3GCA_A	-	-0.05	0.00	0.00	0	150	8	4	4	0	7
3GX2_A	SAM links to Rfam database...	0.58	0.61	0.57	17	1419	15	1	12	2	11
3HAY_E	-	1.00	1.00	1.00	14	910	10	0	0	10	0
3HJW_D	-	1.00	1.00	1.00	16	593	5	0	0	5	0
3IAB_R	-	1.00	1.00	1.00	12	373	4	0	0	4	0
3ID5_D	-	0.54	0.60	0.50	3	223	7	1	2	4	2
3IVN_B	Purine links to Rfam database...	0.45	0.48	0.46	11	879	14	5	8	1	12
3IWN_A	c-di-GMP-I links to Rfam database...	0.19	0.21	0.20	6	1442	24	5	19	0	22
3IZF_C	5S_rRNA links to Rfam database...	0.92	0.94	0.89	33	2603	10	0	4	6	2
3J0L_g	-	-0.02	0.00	0.00	0	170	7	4	2	1	2
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.14	0.18	0.15	2	398	13	1	10	2	9
3J0L_1	-	0.88	0.85	0.92	11	472	5	0	1	4	2
3J0L_h	-	0.98	0.97	1.00	31	2109	2	0	0	2	1
3J0L_7	-	-0.02	0.00	0.00	0	504	15	6	9	0	10
3J0L_2	-	0.25	0.27	0.25	7	2222	29	4	17	8	19
3J16_L	tRNA links to Rfam database...	0.54	0.57	0.52	12	1136	12	4	7	1	9
3JYV_7	tRNA links to Rfam database...	0.25	0.30	0.24	6	1086	20	8	11	1	14
3JYX_4	5_8S_rRNA links to Rfam database...	0.36	0.58	0.23	7	4725	37	19	5	13	5
3JYX_3	5S_rRNA links to Rfam database...	0.46	0.67	0.32	10	2347	28	15	6	7	5
3KTW_C	-	0.55	0.60	0.52	15	1751	20	4	10	6	10
3LA5_A	Purine links to Rfam database...	0.44	0.44	0.48	11	931	12	2	10	0	14
3NDB_M	-	0.29	0.30	0.30	13	3671	35	1	29	5	31
3NKB_B	-	0.68	0.74	0.64	14	713	8	2	6	0	5
3NMU_E	-	0.51	0.67	0.40	2	211	8	1	2	5	1
3O58_3	5_8S_rRNA links to Rfam database...	0.28	0.36	0.22	8	4727	39	14	15	10	14
3O58_2	5S_rRNA links to Rfam database...	0.25	0.29	0.23	9	2715	31	6	24	1	22
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...	0.78	0.80	0.77	40	4788	14	5	7	2	10
3R4F_A	-	0.95	0.95	0.95	21	884	4	0	1	3	1
3R9X_C	-	0.87	0.88	0.88	7	221	5	0	1	4	1
3RKF_A	Purine links to Rfam database...	0.89	0.88	0.91	21	843	3	0	2	1	3
3SD1_A	THF links to Rfam database...	0.43	0.45	0.43	13	1503	17	1	16	0	16
3SIU_F	-	0.53	0.63	0.50	5	135	5	2	3	0	3
3SN2_B	IRE_II links to Rfam database...	0.58	0.58	0.64	7	143	4	0	4	0	5
3TRZ_Z	-	-0.05	0.00	0.00	0	88	4	0	4	0	5
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	-0.05	0.00	0.00	0	102	7	0	6	1	5
3U4M_B	-	0.74	0.77	0.71	17	1252	10	1	6	3	5
3VJR_D	-	1.00	1.00	1.00	12	239	1	0	0	1	0
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.86	0.86	32	2726	9	0	5	4	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4480	45	12	19	14	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4ENB_A	crcB links to Rfam database...	0.78	0.73	0.85	11	459	4	0	2	2	4
4ENC_A	crcB links to Rfam database...	0.34	0.33	0.38	5	483	11	0	8	3	10

^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 RNAsubopt - scored higher in this pairwise comparison

1. Total counts & total scores for RNAsubopt

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

Performance of MCFold - scored lower in this pairwise comparison

1. Total counts & total scores for MCFold

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