CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

Home

Methods

Datasets

Rankings

RNA 2D Atlas

Help

FAQ

Contact us

RSS feeds

Twitter

Overview

Metric	RNASampler(20)		Murlet(20)
MCC	0.751	>	0.693
Average MCC ± 95% Confidence Intervals	0.774 ± 0.073	>	0.690 ± 0.070
Sensitivity	0.663	>	0.594
Positive Predictive Value	0.856	>	0.815
Total TP	594	>	532
Total TN	92168	<	92209
Total FP	209	>	202
Total FP CONTRA	41	>	25
Total FP INCONS	59	<	96
Total FP COMP	109	>	81
Total FN	302	<	364
P-value	3.56938820447e-08

^top

Performance plots

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

^top

Performance of RNASampler(20) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP	594
Total TN	92168
Total FP	209
Total FP CONTRA	41
Total FP INCONS	59
Total FP COMP	109
Total FN	302

Total Scores
MCC	0.751
Average MCC ± 95% Confidence Intervals	0.774 ± 0.073
Sensitivity	0.663
Positive Predictive Value	0.856
Nr of predictions	34

^top

2. Individual counts for RNASampler(20) [ 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
2L94_A	HIV_FE links to Rfam database...	0.94	0.94	0.94	17	339	2	0	1	1	1
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	14	0	0	14	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.60	0.36	1.00	4	1831	2	0	0	2	7
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...	0.34	0.11	1.00	4	2041	0	0	0	0	31
3A2K_C	tRNA links to Rfam database...	0.98	0.95	1.00	21	1087	0	0	0	0	1
3AMU_B	tRNA links to Rfam database...	0.95	0.95	0.95	18	1138	4	0	1	3	1
3G4S_9	5S_rRNA links to Rfam database...	0.73	0.54	1.00	14	2722	4	0	0	4	12
3GX2_A	SAM links to Rfam database...	0.88	0.79	1.00	22	1427	1	0	0	1	6
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...	0.52	0.41	0.65	39	25476	26	15	6	5	56
3IZF_C	5S_rRNA links to Rfam database...	0.92	0.86	1.00	30	2610	2	0	0	2	5
3J20_0	tRNA links to Rfam database...	0.90	0.90	0.90	19	1198	3	1	1	1	2
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.50	0.63	17	2993	12	3	7	2	17
3JYV_7	tRNA links to Rfam database...	0.97	0.95	1.00	19	1092	2	0	0	2	1
3JYX_4	5_8S_rRNA links to Rfam database...	0.61	0.83	0.45	10	4734	26	10	2	14	2
3JYX_3	5S_rRNA links to Rfam database...	0.70	0.60	0.82	9	2367	14	0	2	12	6
3LA5_A	Purine links to Rfam database...	0.89	0.80	1.00	20	934	0	0	0	0	5
3NPB_A	SAM links to Rfam database...	0.75	0.57	1.00	21	2257	5	0	0	5	16
3O58_2	5S_rRNA links to Rfam database...	0.93	0.87	1.00	27	2727	5	0	0	5	4
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.50	0.52	11	4743	19	5	5	9	11
3PDR_A	ykoK links to Rfam database...	0.84	0.76	0.93	38	4799	5	1	2	2	12
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...	0.81	0.69	0.95	20	1512	1	0	1	0	9
3ZEX_C	5_8S_rRNA links to Rfam database...	0.35	0.31	0.39	9	5351	21	3	11	7	20
3ZEX_D	5S_rRNA links to Rfam database...	0.83	0.69	1.00	24	2772	1	0	0	1	11
4A1C_3	5S_rRNA links to Rfam database...	0.90	0.81	1.00	30	2733	0	0	0	0	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.25	0.24	5	4495	30	3	13	14	15
4AOB_A	SAM links to Rfam database...	0.70	0.59	0.85	17	1417	4	0	3	1	12
4ENB_A	crcB links to Rfam database...	0.68	0.47	1.00	7	465	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	0	0	0	0	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.64	0.54	0.76	13	1185	4	0	4	0	11

^top

Performance of Murlet(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	532
Total TN	92209
Total FP	202
Total FP CONTRA	25
Total FP INCONS	96
Total FP COMP	81
Total FN	364

Total Scores
MCC	0.693
Average MCC ± 95% Confidence Intervals	0.690 ± 0.070
Sensitivity	0.594
Positive Predictive Value	0.815
Nr of predictions	34

^top

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
2KDQ_B	mir-TAR links to Rfam database...	0.70	0.50	1.00	5	169	0	0	0	0	5
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
3G4S_9	5S_rRNA links to Rfam database...	0.85	0.77	0.95	20	2715	5	0	1	4	6
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
3J20_0	tRNA links to Rfam database...	0.65	0.62	0.68	13	1200	6	1	5	0	8
3J20_1	tRNA links to Rfam database...	0.69	0.60	0.80	12	1097	4	0	3	1	8
3J2L_3	5S_rRNA links to Rfam database...	0.84	0.74	0.96	25	2994	4	0	1	3	9
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_2	5S_rRNA links to Rfam database...	1.00	1.00	1.00	31	2723	2	0	0	2	0
3O58_3	5_8S_rRNA links to Rfam database...	0.37	0.32	0.44	7	4748	13	4	5	4	15
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
3ZEX_C	5_8S_rRNA links to Rfam database...	0.42	0.38	0.48	11	5351	16	2	10	4	18
3ZEX_D	5S_rRNA links to Rfam database...	0.90	0.86	0.94	30	2764	5	0	2	3	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
4FRG_B	AdoCbl-variant links to Rfam database...	0.19	0.17	0.25	4	1186	12	1	11	0	20

^top

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 RNASampler(20) - scored higher in this pairwise comparison

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

2. Individual counts for RNASampler(20) [ 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 ]