CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	MaxExpect		Mastr(seed)
MCC	0.600	>	0.247
Average MCC ± 95% Confidence Intervals	0.631 ± 0.072	>	0.119 ± 0.086
Sensitivity	0.532	>	0.068
Positive Predictive Value	0.682	<	0.900
Total TP	915	>	117
Total TN	334199	<	335411
Total FP	527	>	15
Total FP CONTRA	58	>	0
Total FP INCONS	369	>	13
Total FP COMP	100	>	2
Total FN	806	<	1604
P-value	3.56938820447e-08

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Performance plots

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

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Performance of MaxExpect - scored higher in this pairwise comparison

1. Total counts & total scores for MaxExpect

Total Base Pair Counts
Total TP	915
Total TN	334199
Total FP	527
Total FP CONTRA	58
Total FP INCONS	369
Total FP COMP	100
Total FN	806

Total Scores
MCC	0.600
Average MCC ± 95% Confidence Intervals	0.631 ± 0.072
Sensitivity	0.532
Positive Predictive Value	0.682
Nr of predictions	48

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KE6_A	K10_TLS links to Rfam database...	0.92	0.89	0.94	17	1110	2	0	1	1	2
2KUR_A	K10_TLS links to Rfam database...	0.90	0.86	0.95	18	1109	1	0	1	0	3
2KUU_A	K10_TLS links to Rfam database...	0.87	0.81	0.94	17	1110	2	0	1	1	4
2KUV_A	K10_TLS links to Rfam database...	0.88	0.82	0.95	18	1109	1	0	1	0	4
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...	0.94	0.89	1.00	16	845	0	0	0	0	2
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
2WRQ_Y	tRNA links to Rfam database...	0.53	0.53	0.53	9	2833	13	5	3	5	8
2WWQ_V	tRNA links to Rfam database...	0.76	0.64	0.90	18	2906	3	0	2	1	10
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.51	0.50	0.53	10	4541	24	0	9	15	10
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.25	0.24	0.27	10	5114	27	1	26	0	32
3A2K_C	tRNA links to Rfam database...	0.42	0.39	0.46	11	2902	13	2	11	0	17
3AKZ_H	tRNA links to Rfam database...	0.84	0.75	0.95	21	2679	1	1	0	0	7
3AMU_B	tRNA links to Rfam database...	0.64	0.59	0.70	16	2980	9	0	7	2	11
3GX2_A	SAM links to Rfam database...	0.77	0.63	0.96	25	4345	2	0	1	1	15
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IYQ_A	tmRNA links to Rfam database...	0.29	0.31	0.27	29	60617	84	19	61	4	65
3IZ4_A	tmRNA links to Rfam database...	0.54	0.46	0.64	61	70781	39	3	31	5	71
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.61	0.83	33	6863	7	1	6	0	21
3J16_L	tRNA links to Rfam database...	0.29	0.23	0.37	7	2756	12	0	12	0	23
3J20_1	tRNA links to Rfam database...	0.73	0.70	0.76	16	2905	5	0	5	0	7
3J20_0	tRNA links to Rfam database...	0.44	0.40	0.50	12	2826	13	0	12	1	18
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.53	0.74	28	7837	12	0	10	2	25
3JYV_7	tRNA links to Rfam database...	0.41	0.31	0.56	10	2832	8	0	8	0	22
3JYX_3	5S_rRNA links to Rfam database...	0.64	0.63	0.65	17	6302	19	1	8	10	10
3JYX_4	5_8S_rRNA links to Rfam database...	0.31	0.30	0.31	10	12214	34	4	18	12	23
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NPB_A	SAM links to Rfam database...	0.71	0.61	0.82	28	6987	9	0	6	3	18
3O58_3	5_8S_rRNA links to Rfam database...	0.35	0.34	0.35	12	12369	35	2	20	13	23
3O58_2	5S_rRNA links to Rfam database...	0.75	0.76	0.74	29	7221	11	3	7	1	9
3PDR_A	ykoK links to Rfam database...	0.76	0.63	0.94	45	12832	5	0	3	2	27
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...	0.58	0.48	0.71	20	3888	8	1	7	0	22
3UZL_B	tRNA links to Rfam database...	0.77	0.62	0.96	23	3546	1	0	1	0	14
3W3S_B	tRNA-Sec links to Rfam database...	0.88	0.78	1.00	31	4722	1	0	0	1	9
3ZEX_C	5_8S_rRNA links to Rfam database...	0.41	0.27	0.64	14	14174	16	2	6	8	38
3ZEX_D	5S_rRNA links to Rfam database...	0.69	0.61	0.79	30	6983	8	1	7	0	19
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	0	6	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11746	41	4	26	11	28
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.31	0.26	0.38	5	1313	8	1	7	0	14
4FRG_B	AdoCbl-variant links to Rfam database...	0.30	0.22	0.41	7	3469	10	1	9	0	25
4FRN_A	AdoCbl-variant links to Rfam database...	0.45	0.36	0.57	13	5128	10	2	8	0	23

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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	117
Total TN	335411
Total FP	15
Total FP CONTRA	0
Total FP INCONS	13
Total FP COMP	2
Total FN	1604

Total Scores
MCC	0.247
Average MCC ± 95% Confidence Intervals	0.119 ± 0.086
Sensitivity	0.068
Positive Predictive Value	0.900
Nr of predictions	48

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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
2KE6_A	K10_TLS links to Rfam database...	0.92	0.84	1.00	16	1112	1	0	0	1	3
2KUR_A	K10_TLS links to Rfam database...	0.79	0.71	0.88	15	1111	2	0	2	0	6
2KUU_A	K10_TLS links to Rfam database...	0.76	0.67	0.88	14	1112	3	0	2	1	7
2KUV_A	K10_TLS links to Rfam database...	0.77	0.68	0.88	15	1111	2	0	2	0	7
2KUW_A	K10_TLS links to Rfam database...	0.52	0.48	0.59	10	1111	7	0	7	0	11
2KX8_A	7SK links to Rfam database...	0.00	0.00	0.00	0	861	0	0	0	0	18
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L94_A	HIV_FE links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	20
2LC8_A	GP_knot1 links to Rfam database...	0.00	0.00	0.00	0	1540	0	0	0	0	20
2WRQ_Y	tRNA links to Rfam database...	0.00	0.00	0.00	0	2850	0	0	0	0	17
2WWQ_V	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	28
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4560	0	0	0	0	20
2XQD_Y	tRNA links to Rfam database...	0.00	0.00	0.00	0	2850	0	0	0	0	27
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5151	0	0	0	0	42
3A2K_C	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	28
3AKZ_H	tRNA links to Rfam database...	0.00	0.00	0.00	0	2701	0	0	0	0	28
3AMU_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3003	0	0	0	0	27
3GX2_A	SAM links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	40
3IVN_B	Purine links to Rfam database...	0.00	0.00	0.00	0	2346	0	0	0	0	31
3IYQ_A	tmRNA links to Rfam database...	0.00	0.00	0.00	0	60726	0	0	0	0	94
3IZ4_A	tmRNA links to Rfam database...	0.00	0.00	0.00	0	70876	0	0	0	0	132
3IZF_C	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	6903	0	0	0	0	54
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	2775	0	0	0	0	30
3J20_1	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	23
3J20_0	tRNA links to Rfam database...	0.00	0.00	0.00	0	2850	0	0	0	0	30
3J2L_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7875	0	0	0	0	53
3JYV_7	tRNA links to Rfam database...	0.00	0.00	0.00	0	2850	0	0	0	0	32
3JYX_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	6328	0	0	0	0	27
3JYX_4	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	12246	0	0	0	0	33
3LA5_A	Purine links to Rfam database...	0.00	0.00	0.00	0	2485	0	0	0	0	34
3NPB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	7021	0	0	0	0	46
3O58_3	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	12403	0	0	0	0	35
3O58_2	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7260	0	0	0	0	38
3PDR_A	ykoK links to Rfam database...	0.00	0.00	0.00	0	12880	0	0	0	0	72
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	2211	0	0	0	0	34
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	3916	0	0	0	0	42
3UZL_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3570	0	0	0	0	37
3W3S_B	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	40
3ZEX_C	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	14196	0	0	0	0	52
3ZEX_D	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7021	0	0	0	0	49
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7140	0	0	0	0	54
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11781	0	0	0	0	33
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	42
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1275	0	0	0	0	19
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1326	0	0	0	0	19
4FRG_B	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	3486	0	0	0	0	32
4FRN_A	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	5151	0	0	0	0	36

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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 MaxExpect - scored higher in this pairwise comparison

1. Total counts & total scores for MaxExpect

2. Individual counts for MaxExpect [ 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 ]