CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Vsfold5		Mastr(seed)
MCC	0.557	>	0.306
Average MCC ± 95% Confidence Intervals	0.618 ± 0.112	>	0.132 ± 0.095
Sensitivity	0.565	>	0.105
Positive Predictive Value	0.557	<	0.899
Total TP	622	>	116
Total TN	112831	<	113818
Total FP	607	>	16
Total FP CONTRA	153	>	0
Total FP INCONS	341	>	13
Total FP COMP	113	>	3
Total FN	478	<	984
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of Vsfold5 and Mastr(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 Vsfold5 and Mastr(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 Vsfold5 and Mastr(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Vsfold5 and Mastr(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 Vsfold5 and Mastr(seed)).

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Performance of Vsfold5 - scored higher in this pairwise comparison

1. Total counts & total scores for Vsfold5

Total Base Pair Counts
Total TP	622
Total TN	112831
Total FP	607
Total FP CONTRA	153
Total FP INCONS	341
Total FP COMP	113
Total FN	478

Total Scores
MCC	0.557
Average MCC ± 95% Confidence Intervals	0.618 ± 0.112
Sensitivity	0.565
Positive Predictive Value	0.557
Nr of predictions	45

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2. Individual counts for Vsfold5 [ 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...	0.95	0.90	1.00	9	165	0	0	0	0	1
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...	0.71	0.63	0.83	15	773	3	0	3	0	9
2L1F_A	Gammaretro_CES links to Rfam database...	0.70	0.61	0.82	14	746	3	0	3	0	9
2L94_A	HIV_FE links to Rfam database...	0.97	0.94	1.00	17	340	1	0	0	1	1
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...	0.94	0.89	1.00	8	1144	13	0	0	13	1
2WWQ_V	tRNA links to Rfam database...	0.78	0.74	0.82	14	1187	4	1	2	1	5
2XKV_B	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	1803	32	17	15	0	11
2XQD_Y	tRNA links to Rfam database...	0.95	0.90	1.00	19	1110	1	0	0	1	2
2XXA_G	Bacteria_small_SRP links to Rfam database...	-0.02	0.00	0.00	0	2014	31	2	29	0	35
2ZZM_B	tRNA links to Rfam database...	0.17	0.20	0.16	3	1339	25	4	12	9	12
2ZZN_D	tRNA links to Rfam database...	0.95	0.95	0.95	21	962	1	1	0	0	1
3A2K_C	tRNA links to Rfam database...	0.95	0.91	1.00	20	1088	0	0	0	0	2
3A3A_A	tRNA-Sec links to Rfam database...	0.95	0.90	1.00	27	1473	0	0	0	0	3
3AKZ_H	tRNA links to Rfam database...	0.97	0.95	1.00	19	1108	1	0	0	1	1
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	8	0	5	3	4
3G4S_9	5S_rRNA links to Rfam database...	0.12	0.15	0.11	4	2699	33	9	24	0	22
3GX2_A	SAM links to Rfam database...	0.61	0.57	0.67	16	1425	9	0	8	1	12
3IVN_B	Purine links to Rfam database...	0.88	0.78	1.00	18	885	0	0	0	0	5
3IYQ_A	tmRNA links to Rfam database...	0.30	0.37	0.24	19	22361	71	36	24	11	32
3IZ4_A	tmRNA links to Rfam database...	0.31	0.31	0.33	29	25448	65	14	45	6	66
3IZF_C	5S_rRNA links to Rfam database...	0.85	0.83	0.88	29	2607	5	0	4	1	6
3J16_L	tRNA links to Rfam database...	0.98	0.95	1.00	20	1139	0	0	0	0	1
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1092	19	4	15	0	20
3JYX_4	5_8S_rRNA links to Rfam database...	0.63	0.83	0.48	10	4735	32	9	2	21	2
3JYX_3	5S_rRNA links to Rfam database...	0.12	0.13	0.11	2	2360	20	6	10	4	13
3LA5_A	Purine links to Rfam database...	-0.02	0.00	0.00	0	938	16	0	16	0	25
3NPB_A	SAM links to Rfam database...	0.62	0.54	0.71	20	2250	10	1	7	2	17
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.59	0.45	13	4735	28	11	5	12	9
3O58_2	5S_rRNA links to Rfam database...	0.50	0.52	0.50	16	2722	19	3	13	3	15
3PDR_A	ykoK links to Rfam database...	0.69	0.64	0.74	32	4797	13	3	8	2	18
3RKF_A	Purine links to Rfam database...	0.90	0.92	0.88	22	841	3	3	0	0	2
3SD1_A	THF links to Rfam database...	0.13	0.14	0.15	4	1507	22	5	17	0	25
3UZL_B	tRNA links to Rfam database...	0.24	0.31	0.20	5	1268	20	9	11	0	11
4A1C_3	5S_rRNA links to Rfam database...	0.29	0.30	0.31	11	2727	26	4	21	1	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.28	8	4487	37	8	13	16	12
4AOB_A	SAM links to Rfam database...	0.21	0.21	0.25	6	1413	19	2	16	1	23
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0

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

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

Total Base Pair Counts
Total TP	116
Total TN	113818
Total FP	16
Total FP CONTRA	0
Total FP INCONS	13
Total FP COMP	3
Total FN	984

Total Scores
MCC	0.306
Average MCC ± 95% Confidence Intervals	0.132 ± 0.095
Sensitivity	0.105
Positive Predictive Value	0.899
Nr of predictions	45

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2. Individual counts for Mastr(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...	0.00	0.00	0.00	0	174	0	0	0	0	10
2KE6_A	K10_TLS links to Rfam database...	0.94	0.89	1.00	16	451	1	0	0	1	2
2KUR_A	K10_TLS links to Rfam database...	0.83	0.79	0.88	15	450	2	0	2	0	4
2KUU_A	K10_TLS links to Rfam database...	0.82	0.78	0.88	14	431	3	0	2	1	4
2KUV_A	K10_TLS links to Rfam database...	0.83	0.79	0.88	15	422	2	0	2	0	4
2KUW_A	K10_TLS links to Rfam database...	0.51	0.50	0.56	9	454	8	0	7	1	9
2KX8_A	7SK links to Rfam database...	0.00	0.00	0.00	0	371	0	0	0	0	16
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
2L94_A	HIV_FE links to Rfam database...	0.00	0.00	0.00	0	357	0	0	0	0	18
2LC8_A	GP_knot1 links to Rfam database...	0.00	0.00	0.00	0	528	0	0	0	0	18
2WRQ_Y	tRNA links to Rfam database...	0.00	0.00	0.00	0	1152	0	0	0	0	9
2WWQ_V	tRNA links to Rfam database...	0.00	0.00	0.00	0	1204	0	0	0	0	19
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	1835	0	0	0	0	11
2XQD_Y	tRNA links to Rfam database...	0.00	0.00	0.00	0	1129	0	0	0	0	21
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	2045	0	0	0	0	35
2ZZM_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	1358	0	0	0	0	15
2ZZN_D	tRNA links to Rfam database...	0.00	0.00	0.00	0	984	0	0	0	0	22
3A2K_C	tRNA links to Rfam database...	0.00	0.00	0.00	0	1108	0	0	0	0	22
3A3A_A	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	1500	0	0	0	0	30
3AKZ_H	tRNA links to Rfam database...	0.00	0.00	0.00	0	1127	0	0	0	0	20
3AMU_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	1157	0	0	0	0	19
3G4S_9	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2736	0	0	0	0	26
3GX2_A	SAM links to Rfam database...	0.00	0.00	0.00	0	1449	0	0	0	0	28
3IVN_B	Purine links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	23
3IYQ_A	tmRNA links to Rfam database...	0.00	0.00	0.00	0	22440	0	0	0	0	51
3IZ4_A	tmRNA links to Rfam database...	0.00	0.00	0.00	0	25536	0	0	0	0	95
3IZF_C	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2640	0	0	0	0	35
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	1159	0	0	0	0	21
3JYV_7	tRNA links to Rfam database...	0.00	0.00	0.00	0	1111	0	0	0	0	20
3JYX_4	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4756	0	0	0	0	12
3JYX_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2378	0	0	0	0	15
3LA5_A	Purine links to Rfam database...	0.00	0.00	0.00	0	954	0	0	0	0	25
3NPB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	2278	0	0	0	0	37
3O58_3	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4764	0	0	0	0	22
3O58_2	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2754	0	0	0	0	31
3PDR_A	ykoK links to Rfam database...	0.00	0.00	0.00	0	4840	0	0	0	0	50
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	866	0	0	0	0	24
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...	0.00	0.00	0.00	0	1293	0	0	0	0	16
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2763	0	0	0	0	37
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4516	0	0	0	0	20
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	1437	0	0	0	0	29
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	472	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	496	0	0	0	0	15

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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 Vsfold5 - scored higher in this pairwise comparison

1. Total counts & total scores for Vsfold5

2. Individual counts for Vsfold5 [ download as .csv ]

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

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

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