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		Alterna
MCC	0.795	>	0.767
Average MCC ± 95% Confidence Intervals	0.789 ± 0.068	>	0.768 ± 0.066
Sensitivity	0.795	>	0.777
Positive Predictive Value	0.805	>	0.769
Total TP	1001	>	978
Total TN	48822	>	48793
Total FP	360	<	419
Total FP CONTRA	54	<	79
Total FP INCONS	188	<	215
Total FP COMP	118	<	125
Total FN	258	<	281
P-value	3.56938820447e-08

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Performance plots

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

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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	1001
Total TN	48822
Total FP	360
Total FP CONTRA	54
Total FP INCONS	188
Total FP COMP	118
Total FN	258

Total Scores
MCC	0.795
Average MCC ± 95% Confidence Intervals	0.789 ± 0.068
Sensitivity	0.795
Positive Predictive Value	0.805
Nr of predictions	89

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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_B	Gammaretro_CES links to Rfam database...	0.96	0.92	1.00	22	769	0	0	0	0	2
2L1F_A	Gammaretro_CES links to Rfam database...	0.95	0.91	1.00	21	742	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
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	-	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_D	-	0.09	0.10	0.11	1	732	13	2	6	5	9
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
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
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
2ZZM_B	tRNA links to Rfam database...	0.29	0.33	0.26	5	1339	22	5	9	8	10
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
3ADB_C	-	0.98	0.97	1.00	32	1787	0	0	0	0	1
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
3J0L_7	-	-0.02	0.00	0.00	0	507	12	2	10	0	10
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_g	-	-0.01	0.00	0.00	0	173	5	1	2	2	2
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
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
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
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...	0.73	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
3UZL_B	tRNA links to Rfam database...	0.49	0.50	0.50	8	1277	15	0	8	7	8

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Performance of Alterna - scored lower in this pairwise comparison

1. Total counts & total scores for Alterna

Total Base Pair Counts
Total TP	978
Total TN	48793
Total FP	419
Total FP CONTRA	79
Total FP INCONS	215
Total FP COMP	125
Total FN	281

Total Scores
MCC	0.767
Average MCC ± 95% Confidence Intervals	0.768 ± 0.066
Sensitivity	0.777
Positive Predictive Value	0.769
Nr of predictions	89

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2. Individual counts for Alterna [ 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...	0.94	0.94	0.94	17	449	2	0	1	1	1
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	1	0	0	1	0
2KMJ_A	-	1.00	1.00	1.00	11	157	0	0	0	0	0
2KPV_A	-	0.56	0.54	0.64	7	202	4	0	4	0	6
2KU0_A	-	0.39	0.42	0.42	5	280	7	2	5	0	7
2KUR_A	K10_TLS links to Rfam database...	0.95	0.95	0.95	18	448	1	0	1	0	1
2KUU_A	K10_TLS links to Rfam database...	0.94	0.94	0.94	17	429	2	0	1	1	1
2KUV_A	K10_TLS links to Rfam database...	0.94	0.95	0.95	18	420	1	0	1	0	1
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...	0.93	0.94	0.94	15	355	1	0	1	0	1
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...	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	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...	0.47	0.44	0.53	8	513	7	0	7	0	10
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
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	-	-0.02	0.00	0.00	0	724	17	8	9	0	10
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...	1.00	1.00	1.00	19	1185	5	0	0	5	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.56	0.64	0.50	7	1821	27	0	7	20	4
2XQD_Y	tRNA links to Rfam database...	0.73	0.71	0.75	15	1109	6	0	5	1	6
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	-	0.53	0.57	0.50	4	536	9	1	3	5	3
2ZY6_A	-	0.69	0.78	0.64	7	265	5	2	2	1	2
2ZZM_B	tRNA links to Rfam database...	0.12	0.13	0.13	2	1342	21	3	11	7	13
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...	0.49	0.55	0.46	12	1082	14	3	11	0	10
3A3A_A	tRNA-Sec links to Rfam database...	0.93	0.87	1.00	26	1474	0	0	0	0	4
3ADB_C	-	0.63	0.64	0.64	21	1786	12	1	11	0	12
3AKZ_H	tRNA links to Rfam database...	0.45	0.50	0.42	10	1103	16	6	8	2	10
3AM1_B	-	0.67	0.69	0.67	20	1436	10	3	7	0	9
3AMU_B	tRNA links to Rfam database...	0.73	0.79	0.68	15	1135	10	0	7	3	4
3DW4_A	-	0.91	0.83	1.00	5	135	3	0	0	3	1
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.56	0.57	0.57	16	1421	13	4	8	1	12
3HAY_E	-	1.00	1.00	1.00	14	910	9	0	0	9	0
3HJW_D	-	0.94	0.94	0.94	15	593	3	0	1	2	1
3IAB_R	-	1.00	1.00	1.00	12	373	4	0	0	4	0
3ID5_D	-	-0.02	0.00	0.00	0	224	5	1	4	0	5
3IVN_B	Purine links to Rfam database...	0.81	0.78	0.86	18	882	3	2	1	0	5
3IWN_A	c-di-GMP-I links to Rfam database...	0.81	0.79	0.85	22	1446	5	1	3	1	6
3J0L_7	-	0.37	0.40	0.36	4	508	9	2	5	2	6
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.18	0.18	0.22	2	402	8	3	4	1	9
3J0L_1	-	0.63	0.62	0.67	8	472	8	0	4	4	5
3J0L_g	-	-0.02	0.00	0.00	0	169	9	3	4	2	2
3J16_L	tRNA links to Rfam database...	0.76	0.76	0.76	16	1138	5	3	2	0	5
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1089	22	4	18	0	20
3KTW_C	-	0.48	0.52	0.46	13	1752	21	2	13	6	12
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.41	0.42	0.42	8	716	11	3	8	0	11
3NMU_E	-	-0.02	0.00	0.00	0	208	10	5	3	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
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...	0.82	0.79	0.86	19	844	3	1	2	0	5
3SD1_A	THF links to Rfam database...	0.55	0.55	0.57	16	1505	12	4	8	0	13
3SIU_F	-	0.69	0.75	0.67	6	136	3	0	3	0	2
3SN2_B	IRE_II links to Rfam database...	0.91	0.83	1.00	10	144	0	0	0	0	2
3TRZ_Z	-	1.00	1.00	1.00	5	87	2	0	0	2	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
3UZL_B	tRNA links to Rfam database...	0.68	0.75	0.63	12	1274	13	4	3	6	4

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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 Alterna - scored lower in this pairwise comparison

1. Total counts & total scores for Alterna

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