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		Murlet(20)
MCC	0.700	>	0.698
Average MCC ± 95% Confidence Intervals	0.711 ± 0.096	>	0.701 ± 0.077
Sensitivity	0.710	>	0.591
Positive Predictive Value	0.696	<	0.831
Total TP	495	>	412
Total TN	74518	<	74733
Total FP	349	>	150
Total FP CONTRA	62	>	21
Total FP INCONS	154	>	63
Total FP COMP	133	>	66
Total FN	202	<	285
P-value	0.605451749002

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Performance plots

Comparison of performance of MaxExpect and Murlet(20). 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 Murlet(20)).
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 Murlet(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for MaxExpect and Murlet(20). 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 Murlet(20)).

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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	495
Total TN	74518
Total FP	349
Total FP CONTRA	62
Total FP INCONS	154
Total FP COMP	133
Total FN	202

Total Scores
MCC	0.700
Average MCC ± 95% Confidence Intervals	0.711 ± 0.096
Sensitivity	0.710
Positive Predictive Value	0.696
Nr of predictions	26

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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
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2WRQ_Y	tRNA links to Rfam database...	0.94	0.89	1.00	8	1144	14	0	0	14	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
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
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
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_3	5_8S_rRNA links to Rfam database...	0.40	0.50	0.33	11	4731	36	8	14	14	11
3O58_2	5S_rRNA links to Rfam database...	0.91	0.94	0.88	29	2721	11	0	4	7	2
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
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 Murlet(20) - scored lower in this pairwise comparison

1. Total counts & total scores for Murlet(20)

Total Base Pair Counts
Total TP	412
Total TN	74733
Total FP	150
Total FP CONTRA	21
Total FP INCONS	63
Total FP COMP	66
Total FN	285

Total Scores
MCC	0.698
Average MCC ± 95% Confidence Intervals	0.701 ± 0.077
Sensitivity	0.591
Positive Predictive Value	0.831
Nr of predictions	26

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2. Individual counts for Murlet(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.51	0.50	0.56	9	341	8	0	7	1	9
2WRQ_Y	tRNA links to Rfam database...	0.63	0.67	0.60	6	1142	13	1	3	9	3
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.60	0.36	1.00	4	1831	3	0	0	3	7
2XQD_Y	tRNA links to Rfam database...	0.88	0.86	0.90	18	1109	3	0	2	1	3
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.44	0.20	1.00	7	2038	0	0	0	0	28
3A2K_C	tRNA links to Rfam database...	0.88	0.86	0.90	19	1087	2	0	2	0	3
3AMU_B	tRNA links to Rfam database...	0.89	0.89	0.89	17	1138	4	0	2	2	2
3GX2_A	SAM links to Rfam database...	0.73	0.54	1.00	15	1434	1	0	0	1	13
3IVN_B	Purine links to Rfam database...	0.80	0.65	1.00	15	888	0	0	0	0	8
3IZ4_A	tmRNA links to Rfam database...	0.46	0.33	0.66	31	25489	22	3	13	6	64
3IZF_C	5S_rRNA links to Rfam database...	0.88	0.83	0.94	29	2609	5	0	2	3	6
3JYV_7	tRNA links to Rfam database...	0.84	0.80	0.89	16	1093	4	0	2	2	4
3JYX_4	5_8S_rRNA links to Rfam database...	0.72	0.75	0.69	9	4743	15	3	1	11	3
3JYX_3	5S_rRNA links to Rfam database...	0.76	0.73	0.79	11	2364	14	0	3	11	4
3LA5_A	Purine links to Rfam database...	0.80	0.64	1.00	16	938	0	0	0	0	9
3NPB_A	SAM links to Rfam database...	0.65	0.43	1.00	16	2262	2	0	0	2	21
3O58_3	5_8S_rRNA links to Rfam database...	0.37	0.32	0.44	7	4748	13	4	5	4	15
3O58_2	5S_rRNA links to Rfam database...	1.00	1.00	1.00	31	2723	2	0	0	2	0
3PDR_A	ykoK links to Rfam database...	0.84	0.76	0.93	38	4799	3	1	2	0	12
3RKF_A	Purine links to Rfam database...	0.81	0.67	1.00	16	850	0	0	0	0	8
3SD1_A	THF links to Rfam database...	0.82	0.83	0.83	24	1504	5	4	1	0	5
4A1C_3	5S_rRNA links to Rfam database...	0.72	0.59	0.88	22	2738	4	0	3	1	15
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.20	5	4491	24	5	15	4	15
4AOB_A	SAM links to Rfam database...	0.87	0.76	1.00	22	1415	3	0	0	3	7
4ENB_A	crcB links to Rfam database...	0.51	0.27	1.00	4	468	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.57	0.33	1.00	5	491	0	0	0	0	10

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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 Murlet(20) - scored lower in this pairwise comparison

1. Total counts & total scores for Murlet(20)

2. Individual counts for Murlet(20) [ download as .csv ]