CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	MXScarna(seed)		RDfolder
MCC	0.809	>	0.637
Average MCC ± 95% Confidence Intervals	0.784 ± 0.094	>	0.642 ± 0.135
Sensitivity	0.754	>	0.604
Positive Predictive Value	0.876	>	0.687
Total TP	466	>	373
Total TN	27676	>	27665
Total FP	127	<	195
Total FP CONTRA	12	<	39
Total FP INCONS	54	<	131
Total FP COMP	61	>	25
Total FN	152	<	245
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of MXScarna(seed) and RDfolder. 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 MXScarna(seed) and RDfolder).
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 MXScarna(seed) and RDfolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for MXScarna(seed) and RDfolder. 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 MXScarna(seed) and RDfolder).

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Performance of MXScarna(seed) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP	466
Total TN	27676
Total FP	127
Total FP CONTRA	12
Total FP INCONS	54
Total FP COMP	61
Total FN	152

Total Scores
MCC	0.809
Average MCC ± 95% Confidence Intervals	0.784 ± 0.094
Sensitivity	0.754
Positive Predictive Value	0.876
Nr of predictions	31

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2. Individual counts for MXScarna(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...	1.00	1.00	1.00	10	164	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	0.91	0.89	0.94	16	450	2	0	1	1	2
2KUR_A	K10_TLS links to Rfam database...	0.92	0.89	0.94	17	449	1	0	1	0	2
2KUU_A	K10_TLS links to Rfam database...	0.91	0.89	0.94	16	430	2	0	1	1	2
2KUV_A	K10_TLS links to Rfam database...	0.92	0.89	0.94	17	421	1	0	1	0	2
2KUW_A	K10_TLS links to Rfam database...	0.78	0.72	0.87	13	455	3	0	2	1	5
2KX8_A	7SK links to Rfam database...	-0.01	0.00	0.00	0	369	2	0	2	0	16
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...	0.93	0.91	0.95	21	741	1	0	1	0	2
2L94_A	HIV_FE links to Rfam database...	0.55	0.56	0.59	10	340	8	0	7	1	8
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	518	12	0	10	2	18
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	12	0	0	12	0
2WWQ_V	tRNA links to Rfam database...	0.70	0.68	0.72	13	1186	7	0	5	2	6
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.78	0.82	0.75	9	1823	20	0	3	17	2
2XQD_Y	tRNA links to Rfam database...	0.85	0.81	0.89	17	1110	3	0	2	1	4
2ZZM_B	tRNA links to Rfam database...	0.81	0.67	1.00	10	1348	9	0	0	9	5
2ZZN_D	tRNA links to Rfam database...	0.95	0.91	1.00	20	964	0	0	0	0	2
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...	0.84	0.77	0.92	23	1475	4	0	2	2	7
3AKZ_H	tRNA links to Rfam database...	1.00	1.00	1.00	20	1107	1	0	0	1	0
3AMU_B	tRNA links to Rfam database...	0.97	0.95	1.00	18	1139	2	0	0	2	1
3GX2_A	SAM links to Rfam database...	0.83	0.82	0.85	23	1422	7	2	2	3	5
3IVN_B	Purine links to Rfam database...	0.69	0.57	0.87	13	888	2	2	0	0	10
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...	0.95	0.90	1.00	18	1093	2	0	0	2	2
3LA5_A	Purine links to Rfam database...	0.82	0.72	0.95	18	935	1	1	0	0	7
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.74	0.76	0.73	22	1503	9	4	4	1	7
4AOB_A	SAM links to Rfam database...	0.71	0.69	0.74	20	1410	10	2	5	3	9
4ENB_A	crcB links to Rfam database...	0.54	0.40	0.75	6	464	2	0	2	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	1	3	0	9

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Performance of RDfolder - scored lower in this pairwise comparison

1. Total counts & total scores for RDfolder

Total Base Pair Counts
Total TP	373
Total TN	27665
Total FP	195
Total FP CONTRA	39
Total FP INCONS	131
Total FP COMP	25
Total FN	245

Total Scores
MCC	0.637
Average MCC ± 95% Confidence Intervals	0.642 ± 0.135
Sensitivity	0.604
Positive Predictive Value	0.687
Nr of predictions	31

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2. Individual counts for RDfolder [ 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...	0.91	0.83	1.00	15	452	1	0	0	1	3
2KUR_A	K10_TLS links to Rfam database...	0.91	0.84	1.00	16	451	0	0	0	0	3
2KUU_A	K10_TLS links to Rfam database...	0.91	0.83	1.00	15	432	1	0	0	1	3
2KUV_A	K10_TLS links to Rfam database...	0.91	0.84	1.00	16	423	0	0	0	0	3
2KUW_A	K10_TLS links to Rfam database...	0.94	0.89	1.00	16	454	0	0	0	0	2
2KX8_A	7SK links to Rfam database...	0.93	0.88	1.00	14	357	0	0	0	0	2
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...	-0.02	0.00	0.00	0	750	13	2	11	0	23
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	514	14	3	11	0	18
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...	0.80	0.74	0.88	14	1188	4	0	2	2	5
2XKV_B	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	1813	22	10	12	0	11
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2ZZM_B	tRNA links to Rfam database...	0.15	0.20	0.13	3	1334	21	7	14	0	12
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	2	2	0	0	1
3A2K_C	tRNA links to Rfam database...	0.98	0.95	1.00	21	1087	0	0	0	0	1
3A3A_A	tRNA-Sec links to Rfam database...	0.59	0.50	0.71	15	1479	6	0	6	0	15
3AKZ_H	tRNA links to Rfam database...	0.53	0.55	0.52	11	1106	12	1	9	2	9
3AMU_B	tRNA links to Rfam database...	0.20	0.21	0.22	4	1139	16	4	10	2	15
3GX2_A	SAM links to Rfam database...	0.60	0.57	0.64	16	1424	10	2	7	1	12
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3J16_L	tRNA links to Rfam database...	0.26	0.24	0.31	5	1143	11	0	11	0	16
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1091	20	4	16	0	20
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
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...	0.35	0.24	0.54	7	1520	6	1	5	0	22
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ENB_A	crcB links to Rfam database...	0.48	0.40	0.60	6	462	4	0	4	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	0	4	0	9

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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 MXScarna(seed) - scored higher in this pairwise comparison

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

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

Performance of RDfolder - scored lower in this pairwise comparison

1. Total counts & total scores for RDfolder

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