CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	CentroidAlifold(20)		MXScarna(20)
MCC	0.682	>	0.611
Average MCC ± 95% Confidence Intervals	0.670 ± 0.066	>	0.610 ± 0.065
Sensitivity	0.529	>	0.510
Positive Predictive Value	0.882	>	0.736
Total TP	760	>	733
Total TN	276058	>	275924
Total FP	140	<	366
Total FP CONTRA	16	<	47
Total FP INCONS	86	<	216
Total FP COMP	38	<	103
Total FN	676	<	703
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of CentroidAlifold(20) and MXScarna(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 CentroidAlifold(20) and MXScarna(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 CentroidAlifold(20) and MXScarna(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(20) and MXScarna(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 CentroidAlifold(20) and MXScarna(20)).

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

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

Total Base Pair Counts
Total TP	760
Total TN	276058
Total FP	140
Total FP CONTRA	16
Total FP INCONS	86
Total FP COMP	38
Total FN	676

Total Scores
MCC	0.682
Average MCC ± 95% Confidence Intervals	0.670 ± 0.066
Sensitivity	0.529
Positive Predictive Value	0.882
Nr of predictions	36

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	11	5	3	3	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...	0.86	0.74	1.00	20	2983	1	0	0	1	7
3GX2_A	SAM links to Rfam database...	0.77	0.60	1.00	24	4347	1	0	0	1	16
3IVN_B	Purine links to Rfam database...	0.78	0.65	0.95	20	2325	1	1	0	0	11
3IZ4_A	tmRNA links to Rfam database...	0.58	0.39	0.88	51	70818	7	3	4	0	81
3IZF_C	5S_rRNA links to Rfam database...	0.75	0.61	0.92	33	6867	4	0	3	1	21
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	1	0	0	1	9
3J2L_3	5S_rRNA links to Rfam database...	0.76	0.58	1.00	31	7844	2	0	0	2	22
3J3D_C	tRNA links to Rfam database...	0.82	0.71	0.95	20	2754	1	0	1	0	8
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7499	4	0	4	0	33
3J3E_7	5S_rRNA links to Rfam database...	0.64	0.56	0.75	30	7100	10	0	10	0	24
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.25	0.60	9	12231	6	1	5	0	27
3J3F_7	5S_rRNA links to Rfam database...	0.79	0.68	0.92	34	7223	4	0	3	1	16
3J3V_B	5S_rRNA links to Rfam database...	0.66	0.47	0.93	27	6992	2	0	2	0	30
3JYV_7	tRNA links to Rfam database...	0.81	0.66	1.00	21	2829	0	0	0	0	11
3JYX_3	5S_rRNA links to Rfam database...	0.61	0.56	0.68	15	6306	20	0	7	13	12
3JYX_4	5_8S_rRNA links to Rfam database...	0.39	0.27	0.56	9	12230	9	0	7	2	24
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...	0.70	0.54	0.89	25	6993	5	1	2	2	21
3O58_3	5_8S_rRNA links to Rfam database...	0.54	0.31	0.92	11	12391	1	0	1	0	24
3O58_2	5S_rRNA links to Rfam database...	0.78	0.76	0.81	29	7224	9	2	5	2	9
3PDR_A	ykoK links to Rfam database...	0.76	0.63	0.94	45	12832	5	0	3	2	27
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.71	0.52	0.96	22	3893	1	0	1	0	20
3ZEX_D	5S_rRNA links to Rfam database...	0.80	0.69	0.92	34	6984	3	0	3	0	15
3ZEX_C	5_8S_rRNA links to Rfam database...	0.38	0.21	0.69	11	14180	5	1	4	0	41
3ZND_W	tRNA links to Rfam database...	0.47	0.43	0.53	10	2984	12	0	9	3	13
4A1C_3	5S_rRNA links to Rfam database...	0.76	0.63	0.92	34	7103	4	0	3	1	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.15	0.45	5	11770	8	1	5	2	28
4AOB_A	SAM links to Rfam database...	0.75	0.57	1.00	24	4347	1	0	0	1	18
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1319	0	0	0	0	12
4FRG_B	AdoCbl-variant links to Rfam database...	0.69	0.53	0.89	17	3467	2	1	1	0	15

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

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

Total Base Pair Counts
Total TP	733
Total TN	275924
Total FP	366
Total FP CONTRA	47
Total FP INCONS	216
Total FP COMP	103
Total FN	703

Total Scores
MCC	0.611
Average MCC ± 95% Confidence Intervals	0.610 ± 0.065
Sensitivity	0.510
Positive Predictive Value	0.736
Nr of predictions	36

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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...	0.66	0.57	0.76	16	2905	6	1	4	1	12
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	2	0	0	2	7
3GX2_A	SAM links to Rfam database...	0.70	0.58	0.85	23	4344	5	0	4	1	17
3IVN_B	Purine links to Rfam database...	0.74	0.58	0.95	18	2327	1	1	0	0	13
3IZ4_A	tmRNA links to Rfam database...	0.51	0.41	0.64	54	70791	32	7	24	1	78
3IZF_C	5S_rRNA links to Rfam database...	0.67	0.59	0.76	32	6861	11	1	9	1	22
3J20_1	tRNA links to Rfam database...	0.93	0.87	1.00	20	2906	0	0	0	0	3
3J20_0	tRNA links to Rfam database...	0.82	0.67	1.00	20	2830	0	0	0	0	10
3J2L_3	5S_rRNA links to Rfam database...	0.54	0.42	0.71	22	7844	11	1	8	2	31
3J3D_C	tRNA links to Rfam database...	0.82	0.71	0.95	20	2754	1	0	1	0	8
3J3E_8	5_8S_rRNA links to Rfam database...	0.14	0.09	0.23	3	7490	15	2	8	5	30
3J3E_7	5S_rRNA links to Rfam database...	0.61	0.54	0.69	29	7098	13	2	11	0	25
3J3F_8	5_8S_rRNA links to Rfam database...	0.43	0.36	0.52	13	12221	26	2	10	14	23
3J3F_7	5S_rRNA links to Rfam database...	0.66	0.60	0.73	30	7219	12	1	10	1	20
3J3V_B	5S_rRNA links to Rfam database...	0.74	0.61	0.90	35	6982	4	1	3	0	22
3JYV_7	tRNA links to Rfam database...	0.79	0.63	1.00	20	2830	0	0	0	0	12
3JYX_3	5S_rRNA links to Rfam database...	0.55	0.52	0.58	14	6304	23	0	10	13	13
3JYX_4	5_8S_rRNA links to Rfam database...	0.33	0.30	0.37	10	12219	32	2	15	15	23
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...	0.69	0.59	0.82	27	6988	9	1	5	3	19
3O58_3	5_8S_rRNA links to Rfam database...	0.52	0.40	0.67	14	12382	17	2	5	10	21
3O58_2	5S_rRNA links to Rfam database...	0.74	0.74	0.74	28	7222	13	4	6	3	10
3PDR_A	ykoK links to Rfam database...	0.71	0.57	0.89	41	12834	9	0	5	4	31
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.63	0.55	0.74	23	3885	8	2	6	0	19
3ZEX_D	5S_rRNA links to Rfam database...	0.68	0.63	0.74	31	6979	11	2	9	0	18
3ZEX_C	5_8S_rRNA links to Rfam database...	0.31	0.21	0.46	11	14172	13	2	11	0	41
3ZND_W	tRNA links to Rfam database...	0.37	0.35	0.40	8	2983	15	2	10	3	15
4A1C_3	5S_rRNA links to Rfam database...	0.64	0.56	0.75	30	7100	11	2	8	1	24
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.21	5	11757	36	2	17	17	28
4AOB_A	SAM links to Rfam database...	0.62	0.55	0.72	23	4339	10	0	9	1	19
4ENB_A	crcB links to Rfam database...	0.26	0.11	0.67	2	1272	1	0	1	0	17
4ENC_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1319	0	0	0	0	12
4FRG_B	AdoCbl-variant links to Rfam database...	0.55	0.44	0.70	14	3466	6	2	4	0	18

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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 CentroidAlifold(20) - scored higher in this pairwise comparison

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

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

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

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

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