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	0.703	>	0.322
Average MCC ± 95% Confidence Intervals	0.743 ± 0.089	>	0.148 ± 0.106
Sensitivity	0.725	>	0.116
Positive Predictive Value	0.687	<	0.899
Total TP	723	>	116
Total TN	106143	<	107066
Total FP	493	>	16
Total FP CONTRA	106	>	0
Total FP INCONS	223	>	13
Total FP COMP	164	>	3
Total FN	274	<	881
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)).
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)).

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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	723
Total TN	106143
Total FP	493
Total FP CONTRA	106
Total FP INCONS	223
Total FP COMP	164
Total FN	274

Total Scores
MCC	0.703
Average MCC ± 95% Confidence Intervals	0.743 ± 0.089
Sensitivity	0.725
Positive Predictive Value	0.687
Nr of predictions	40

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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...	0.94	0.94	0.94	17	449	2	0	1	1	1
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...	0.94	0.94	0.94	17	452	2	0	1	1	1
2KX8_A	7SK links to Rfam database...	1.00	1.00	1.00	16	355	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
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	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
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
2WRQ_Y	tRNA links to Rfam database...	0.94	0.89	1.00	8	1144	14	0	0	14	1
2WWQ_V	tRNA links to Rfam database...	0.97	0.95	1.00	18	1186	3	0	0	3	1
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	26	0	6	20	3
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.24	0.26	0.25	9	2009	28	1	26	1	26
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3AKZ_H	tRNA links to Rfam database...	1.00	1.00	1.00	20	1107	2	0	0	2	0
3AMU_B	tRNA links to Rfam database...	0.73	0.79	0.68	15	1135	10	0	7	3	4
3GX2_A	SAM links to Rfam database...	0.93	0.89	0.96	25	1423	2	1	0	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...	0.24	0.33	0.17	17	22342	96	41	40	15	34
3IZ4_A	tmRNA links to Rfam database...	0.61	0.61	0.62	58	25442	42	14	22	6	37
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	8	0	5	3	3
3J16_L	tRNA links to Rfam database...	0.34	0.33	0.37	7	1140	12	0	12	0	14
3JYV_7	tRNA links to Rfam database...	0.48	0.45	0.53	9	1094	9	3	5	1	11
3JYX_4	5_8S_rRNA links to Rfam database...	0.55	0.83	0.37	10	4729	34	14	3	17	2
3JYX_3	5S_rRNA links to Rfam database...	0.77	0.80	0.75	12	2362	24	0	4	20	3
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NPB_A	SAM links to Rfam database...	0.77	0.73	0.82	27	2245	10	0	6	4	10
3O58_2	5S_rRNA links to Rfam database...	0.91	0.94	0.88	29	2721	11	0	4	7	2
3O58_3	5_8S_rRNA links to Rfam database...	0.40	0.50	0.33	11	4731	36	8	14	14	11
3PDR_A	ykoK links to Rfam database...	0.92	0.90	0.94	45	4792	5	1	2	2	5
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...	0.70	0.69	0.71	20	1505	8	3	5	0	9
3UZL_B	tRNA links to Rfam database...	1.00	1.00	1.00	16	1277	8	0	0	8	0
4A1C_3	5S_rRNA links to Rfam database...	0.83	0.81	0.86	30	2728	7	0	5	2	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	41	10	17	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	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.36	0.33	0.42	5	484	8	0	7	1	10

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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	107066
Total FP	16
Total FP CONTRA	0
Total FP INCONS	13
Total FP COMP	3
Total FN	881

Total Scores
MCC	0.322
Average MCC ± 95% Confidence Intervals	0.148 ± 0.106
Sensitivity	0.116
Positive Predictive Value	0.899
Nr of predictions	40

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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...	0.94	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_A	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	23	740	0	0	0	0	0
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	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
3A2K_C	tRNA links to Rfam database...	0.00	0.00	0.00	0	1108	0	0	0	0	22
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
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_2	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2754	0	0	0	0	31
3O58_3	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4764	0	0	0	0	22
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 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 ]