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)		McQFold
MCC	0.612	>	0.506
Average MCC ± 95% Confidence Intervals	0.633 ± 0.067	>	0.548 ± 0.094
Sensitivity	0.471	>	0.433
Positive Predictive Value	0.799	>	0.598
Total TP	708	>	651
Total TN	283821	>	283618
Total FP	252	<	499
Total FP CONTRA	28	<	63
Total FP INCONS	150	<	375
Total FP COMP	74	>	61
Total FN	796	<	853
P-value	3.56938820447e-08

^top

Performance plots

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

^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	708
Total TN	283821
Total FP	252
Total FP CONTRA	28
Total FP INCONS	150
Total FP COMP	74
Total FN	796

Total Scores
MCC	0.612
Average MCC ± 95% Confidence Intervals	0.633 ± 0.067
Sensitivity	0.471
Positive Predictive Value	0.799
Nr of predictions	38

^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...	0.95	0.91	1.00	10	396	0	0	0	0	1
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
3A2K_C	tRNA links to Rfam database...	0.86	0.75	1.00	21	2905	0	0	0	0	7
3AMU_B	tRNA links to Rfam database...	0.82	0.70	0.95	19	2983	3	0	1	2	8
3G4S_9	5S_rRNA links to Rfam database...	0.50	0.28	0.89	16	7363	2	1	1	0	41
3GX2_A	SAM links to Rfam database...	0.74	0.55	1.00	22	4349	1	0	0	1	18
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IZ4_A	tmRNA links to Rfam database...	0.47	0.32	0.69	42	70815	23	6	13	4	90
3IZF_C	5S_rRNA links to Rfam database...	0.74	0.57	0.97	31	6871	1	0	1	0	23
3J20_0	tRNA links to Rfam database...	0.80	0.67	0.95	20	2829	2	0	1	1	10
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J2L_3	5S_rRNA links to Rfam database...	0.45	0.32	0.63	17	7848	12	1	9	2	36
3J3D_C	tRNA links to Rfam database...	0.82	0.71	0.95	20	2754	1	0	1	0	8
3J3E_7	5S_rRNA links to Rfam database...	0.62	0.48	0.81	26	7108	6	0	6	0	28
3J3E_8	5_8S_rRNA links to Rfam database...	0.12	0.09	0.18	3	7486	21	2	12	7	30
3J3F_7	5S_rRNA links to Rfam database...	0.66	0.52	0.84	26	7229	5	0	5	0	24
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.33	0.46	12	12220	17	1	13	3	24
3J3V_B	5S_rRNA links to Rfam database...	0.63	0.42	0.96	24	6996	1	0	1	0	33
3JYV_7	tRNA links to Rfam database...	0.81	0.66	1.00	21	2829	0	0	0	0	11
3JYX_4	5_8S_rRNA links to Rfam database...	0.32	0.30	0.34	10	12217	26	4	15	7	23
3JYX_3	5S_rRNA links to Rfam database...	0.58	0.44	0.75	12	6312	11	0	4	7	15
3LA5_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2465	0	0	0	0	14
3NPB_A	SAM links to Rfam database...	0.68	0.48	0.96	22	6998	4	1	0	3	24
3O58_2	5S_rRNA links to Rfam database...	0.79	0.71	0.87	27	7229	5	2	2	1	11
3O58_3	5_8S_rRNA links to Rfam database...	0.43	0.34	0.55	12	12381	18	2	8	8	23
3PDR_A	ykoK links to Rfam database...	0.70	0.53	0.93	38	12839	5	0	3	2	34
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...	0.67	0.48	0.95	20	3895	1	0	1	0	22
3ZEX_D	5S_rRNA links to Rfam database...	0.68	0.49	0.96	24	6996	1	0	1	0	25
3ZEX_C	5_8S_rRNA links to Rfam database...	0.27	0.19	0.38	10	14170	20	1	15	4	42
3ZND_W	tRNA links to Rfam database...	0.41	0.39	0.43	9	2982	15	2	10	3	14
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.23	5	11759	30	0	17	13	28
4A1C_3	5S_rRNA links to Rfam database...	0.74	0.56	1.00	30	7110	0	0	0	0	24
4AOB_A	SAM links to Rfam database...	0.58	0.40	0.85	17	4351	4	0	3	1	25
4ENB_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1268	0	0	0	0	12
4ENC_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1315	0	0	0	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.55	0.41	0.76	13	3469	4	0	4	0	19

^top

Performance of McQFold - scored lower in this pairwise comparison

1. Total counts & total scores for McQFold

Total Base Pair Counts
Total TP	651
Total TN	283618
Total FP	499
Total FP CONTRA	63
Total FP INCONS	375
Total FP COMP	61
Total FN	853

Total Scores
MCC	0.506
Average MCC ± 95% Confidence Intervals	0.548 ± 0.094
Sensitivity	0.433
Positive Predictive Value	0.598
Nr of predictions	38

^top

2. Individual counts for McQFold [ 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...	0.95	0.91	1.00	10	396	0	0	0	0	1
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
3A2K_C	tRNA links to Rfam database...	0.86	0.75	1.00	21	2905	0	0	0	0	7
3AMU_B	tRNA links to Rfam database...	0.75	0.59	0.94	16	2986	3	0	1	2	11
3G4S_9	5S_rRNA links to Rfam database...	0.27	0.21	0.36	12	7348	21	1	20	0	45
3GX2_A	SAM links to Rfam database...	0.47	0.40	0.57	16	4343	13	1	11	1	24
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IZ4_A	tmRNA links to Rfam database...	0.42	0.36	0.49	47	70780	53	6	43	4	85
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	6867	6	0	6	0	24
3J20_0	tRNA links to Rfam database...	0.66	0.57	0.77	17	2828	6	1	4	1	13
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.43	0.72	23	7843	11	0	9	2	30
3J3D_C	tRNA links to Rfam database...	0.82	0.71	0.95	20	2754	1	0	1	0	8
3J3E_7	5S_rRNA links to Rfam database...	0.46	0.37	0.59	20	7106	14	1	13	0	34
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7479	36	3	21	12	33
3J3F_7	5S_rRNA links to Rfam database...	0.18	0.16	0.22	8	7223	29	1	28	0	42
3J3F_8	5_8S_rRNA links to Rfam database...	0.30	0.31	0.30	11	12209	38	4	22	12	25
3J3V_B	5S_rRNA links to Rfam database...	0.49	0.33	0.73	19	6995	7	0	7	0	38
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2830	20	0	20	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.20	0.21	0.19	7	12210	33	8	21	4	26
3JYX_3	5S_rRNA links to Rfam database...	0.21	0.22	0.20	6	6298	24	9	15	0	21
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...	0.81	0.67	0.97	31	6989	4	1	0	3	15
3O58_2	5S_rRNA links to Rfam database...	0.83	0.71	0.96	27	7232	2	0	1	1	11
3O58_3	5_8S_rRNA links to Rfam database...	0.26	0.26	0.26	9	12368	26	10	16	0	26
3PDR_A	ykoK links to Rfam database...	0.69	0.56	0.87	40	12834	9	0	6	3	32
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...	0.71	0.60	0.86	25	3887	4	0	4	0	17
3ZEX_D	5S_rRNA links to Rfam database...	0.69	0.53	0.90	26	6992	3	1	2	0	23
3ZEX_C	5_8S_rRNA links to Rfam database...	0.27	0.21	0.34	11	14164	24	2	19	3	41
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	23	1	20	2	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11748	33	5	23	5	28
4A1C_3	5S_rRNA links to Rfam database...	0.25	0.22	0.29	12	7099	29	1	28	0	42
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.81	0.66	1.00	21	3465	0	0	0	0	11

^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 McQFold - scored lower in this pairwise comparison

1. Total counts & total scores for McQFold

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