CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAshapes		RSpredict(seed)
MCC	0.680	>	0.316
Average MCC ± 95% Confidence Intervals	0.704 ± 0.070	>	0.246 ± 0.085
Sensitivity	0.703	>	0.179
Positive Predictive Value	0.663	>	0.572
Total TP	1043	>	265
Total TN	146296	<	147405
Total FP	775	>	228
Total FP CONTRA	160	>	37
Total FP INCONS	369	>	161
Total FP COMP	246	>	30
Total FN	441	<	1219
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of RNAshapes and RSpredict(seed). 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 RNAshapes and RSpredict(seed)).
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 RNAshapes and RSpredict(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAshapes and RSpredict(seed). 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 RNAshapes and RSpredict(seed)).

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Performance of RNAshapes - scored higher in this pairwise comparison

1. Total counts & total scores for RNAshapes

Total Base Pair Counts
Total TP	1043
Total TN	146296
Total FP	775
Total FP CONTRA	160
Total FP INCONS	369
Total FP COMP	246
Total FN	441

Total Scores
MCC	0.680
Average MCC ± 95% Confidence Intervals	0.704 ± 0.070
Sensitivity	0.703
Positive Predictive Value	0.663
Nr of predictions	60

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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
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...	0.97	0.94	1.00	15	356	0	0	0	0	1
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	768	0	0	0	0	1
2L1F_A	Gammaretro_CES links to Rfam database...	0.89	0.87	0.91	20	741	2	0	2	0	3
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	0	5	0	7
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	13	0	0	13	0
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	24	0	6	18	3
2XQD_Y	tRNA links to Rfam database...	0.70	0.67	0.74	14	1110	6	0	5	1	7
2XXA_G	Bacteria_small_SRP links to Rfam database...	1.00	1.00	1.00	35	2010	1	0	0	1	0
2ZZM_B	tRNA links to Rfam database...	0.05	0.07	0.06	1	1340	25	4	13	8	14
2ZZN_D	tRNA links to Rfam database...	0.77	0.77	0.77	17	962	5	1	4	0	5
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...	0.84	0.80	0.89	24	1473	3	0	3	0	6
3AKZ_H	tRNA links to Rfam database...	0.78	0.80	0.76	16	1106	7	2	3	2	4
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3GX2_A	SAM links to Rfam database...	0.91	0.89	0.93	25	1422	3	1	1	1	3
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IYQ_A	tmRNA links to Rfam database...	0.19	0.27	0.14	14	22340	95	43	43	9	37
3IZ4_A	tmRNA links to Rfam database...	0.57	0.58	0.56	55	25437	50	16	28	6	40
3IZF_C	5S_rRNA links to Rfam database...	0.76	0.77	0.75	27	2604	14	0	9	5	8
3J16_L	tRNA links to Rfam database...	0.59	0.57	0.63	12	1140	7	0	7	0	9
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J20_0	tRNA links to Rfam database...	0.51	0.57	0.48	12	1194	14	3	10	1	9
3J2L_3	5S_rRNA links to Rfam database...	0.77	0.79	0.75	27	2984	14	1	8	5	7
3J3D_C	tRNA links to Rfam database...	0.63	0.68	0.59	13	946	9	3	6	0	6
3J3E_8	5_8S_rRNA links to Rfam database...	0.26	0.33	0.21	5	2718	29	6	13	10	10
3J3E_7	5S_rRNA links to Rfam database...	0.64	0.65	0.65	22	2707	16	1	11	4	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.42	0.26	8	4730	42	11	12	19	11
3J3F_7	5S_rRNA links to Rfam database...	0.83	0.81	0.85	29	2900	7	0	5	2	7
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1092	20	1	18	1	20
3JYX_4	5_8S_rRNA links to Rfam database...	0.61	0.83	0.45	10	4734	35	10	2	23	2
3JYX_3	5S_rRNA links to Rfam database...	0.77	0.80	0.75	12	2362	26	0	4	22	3
3LA5_A	Purine links to Rfam database...	0.89	0.80	1.00	20	934	0	0	0	0	5
3NPB_A	SAM links to Rfam database...	0.84	0.76	0.93	28	2248	5	1	1	3	9
3O58_2	5S_rRNA links to Rfam database...	0.73	0.74	0.72	23	2722	18	0	9	9	8
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	38	6	15	17	11
3PDR_A	ykoK links to Rfam database...	0.80	0.80	0.80	40	4790	12	3	7	2	10
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
3UZL_B	tRNA links to Rfam database...	0.43	0.50	0.38	8	1272	17	4	9	4	8
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.60	0.58	0.63	19	1959	12	2	9	1	14
3ZEX_D	5S_rRNA links to Rfam database...	0.86	0.80	0.93	28	2766	6	0	2	4	7
3ZEX_C	5_8S_rRNA links to Rfam database...	0.29	0.34	0.26	10	5335	42	5	24	13	19
3ZND_W	tRNA links to Rfam database...	0.24	0.38	0.16	3	1172	24	9	7	8	5
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.84	0.89	31	2728	7	0	4	3	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	41	11	16	14	15
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.36	0.38	0.38	9	1178	15	2	13	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.59	0.57	0.62	16	1822	10	2	8	0	12
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5

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Performance of RSpredict(seed) - scored lower in this pairwise comparison

1. Total counts & total scores for RSpredict(seed)

Total Base Pair Counts
Total TP	265
Total TN	147405
Total FP	228
Total FP CONTRA	37
Total FP INCONS	161
Total FP COMP	30
Total FN	1219

Total Scores
MCC	0.316
Average MCC ± 95% Confidence Intervals	0.246 ± 0.085
Sensitivity	0.179
Positive Predictive Value	0.572
Nr of predictions	60

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2. Individual counts for RSpredict(seed) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.89	0.80	1.00	8	166	0	0	0	0	2
2KE6_A	K10_TLS links to Rfam database...	0.85	0.78	0.93	14	452	2	0	1	1	4
2KUR_A	K10_TLS links to Rfam database...	0.86	0.79	0.94	15	451	1	0	1	0	4
2KUU_A	K10_TLS links to Rfam database...	0.85	0.78	0.93	14	432	2	0	1	1	4
2KUV_A	K10_TLS links to Rfam database...	0.85	0.79	0.94	15	423	1	0	1	0	4
2KUW_A	K10_TLS links to Rfam database...	0.75	0.67	0.86	12	456	3	0	2	1	6
2KX8_A	7SK links to Rfam database...	-0.01	0.00	0.00	0	370	1	0	1	0	16
2L1F_B	Gammaretro_CES links to Rfam database...	0.87	0.83	0.91	20	769	2	0	2	0	4
2L1F_A	Gammaretro_CES links to Rfam database...	0.81	0.78	0.86	18	742	3	0	3	0	5
2L94_A	HIV_FE links to Rfam database...	0.55	0.50	0.64	9	343	6	0	5	1	9
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	515	13	0	13	0	18
2WRQ_Y	tRNA links to Rfam database...	0.00	0.00	0.00	0	1150	3	1	1	1	9
2WWQ_V	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1199	6	0	5	1	19
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.38	0.36	0.40	4	1825	8	4	2	2	7
2XQD_Y	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1124	5	0	5	0	21
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.37	0.20	0.70	7	2035	3	0	3	0	28
2ZZM_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	1358	4	0	0	4	15
2ZZN_D	tRNA links to Rfam database...	0.38	0.18	0.80	4	979	1	1	0	0	18
3A2K_C	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1106	2	0	2	0	22
3A3A_A	tRNA-Sec links to Rfam database...	0.53	0.37	0.79	11	1486	3	0	3	0	19
3AKZ_H	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1125	2	0	2	0	20
3AMU_B	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1155	2	0	2	0	19
3GX2_A	SAM links to Rfam database...	0.42	0.21	0.86	6	1442	1	0	1	0	22
3IVN_B	Purine links to Rfam database...	0.81	0.70	0.94	16	886	1	1	0	0	7
3IYQ_A	tmRNA links to Rfam database...	0.16	0.10	0.26	5	22421	21	10	4	7	46
3IZ4_A	tmRNA links to Rfam database...	0.26	0.11	0.63	10	25520	7	2	4	1	85
3IZF_C	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2635	5	0	5	0	35
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	1158	1	0	1	0	21
3J20_1	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1108	5	0	4	1	20
3J20_0	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1215	4	0	4	0	21
3J2L_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	3015	5	0	5	0	34
3J3D_C	tRNA links to Rfam database...	-0.01	0.00	0.00	0	964	4	1	3	0	19
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2742	0	0	0	0	15
3J3E_7	5S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2733	8	1	7	0	34
3J3F_8	5_8S_rRNA links to Rfam database...	0.19	0.11	0.33	2	4755	5	3	1	1	17
3J3F_7	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2930	4	1	3	0	36
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1108	4	0	3	1	20
3JYX_4	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4754	5	0	2	3	12
3JYX_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2373	5	1	4	0	15
3LA5_A	Purine links to Rfam database...	0.82	0.68	1.00	17	937	0	0	0	0	8
3NPB_A	SAM links to Rfam database...	-0.01	0.00	0.00	0	2274	4	0	4	0	37
3O58_2	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2751	3	0	3	0	31
3O58_3	5_8S_rRNA links to Rfam database...	0.28	0.14	0.60	3	4759	2	0	2	0	19
3PDR_A	ykoK links to Rfam database...	0.00	0.00	0.00	0	4832	8	0	8	0	50
3RKF_A	Purine links to Rfam database...	0.84	0.75	0.95	18	847	1	1	0	0	6
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	1533	0	0	0	0	29
3UZL_B	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1287	6	3	3	0	16
3W1K_J	tRNA-Sec links to Rfam database...	0.57	0.35	0.92	11	1666	1	0	1	0	20
3W3S_B	tRNA-Sec links to Rfam database...	0.45	0.36	0.57	12	1968	10	1	8	1	21
3ZEX_D	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2794	2	0	2	0	35
3ZEX_C	5_8S_rRNA links to Rfam database...	0.13	0.07	0.25	2	5366	6	2	4	0	27
3ZND_W	tRNA links to Rfam database...	0.00	0.00	0.00	0	1189	4	0	2	2	8
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2759	4	2	2	0	37
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4512	5	2	2	1	20
4AOB_A	SAM links to Rfam database...	0.42	0.21	0.86	6	1430	1	0	1	0	23
4ENB_A	crcB links to Rfam database...	0.34	0.20	0.60	3	467	2	0	2	0	12
4ENC_A	crcB links to Rfam database...	0.34	0.20	0.60	3	491	2	0	2	0	12
4FRG_B	AdoCbl-variant links to Rfam database...	-0.01	0.00	0.00	0	1200	2	0	2	0	24
4FRN_A	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	1845	3	0	3	0	28
4JF2_A	preQ1-II links to Rfam database...	-0.01	0.00	0.00	0	1078	4	0	4	0	24

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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 RNAshapes - scored higher in this pairwise comparison

1. Total counts & total scores for RNAshapes

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

Performance of RSpredict(seed) - scored lower in this pairwise comparison

1. Total counts & total scores for RSpredict(seed)

2. Individual counts for RSpredict(seed) [ download as .csv ]