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)		CentroidAlifold(seed)
MCC	0.671	>	0.605
Average MCC ± 95% Confidence Intervals	0.660 ± 0.065	>	0.566 ± 0.067
Sensitivity	0.560	>	0.419
Positive Predictive Value	0.807	<	0.878
Total TP	841	>	629
Total TN	295867	<	296193
Total FP	285	>	122
Total FP CONTRA	37	>	14
Total FP INCONS	164	>	73
Total FP COMP	84	>	35
Total FN	661	<	873
P-value	3.56938820447e-08

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Performance plots

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

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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	841
Total TN	295867
Total FP	285
Total FP CONTRA	37
Total FP INCONS	164
Total FP COMP	84
Total FN	661

Total Scores
MCC	0.671
Average MCC ± 95% Confidence Intervals	0.660 ± 0.065
Sensitivity	0.560
Positive Predictive Value	0.807
Nr of predictions	43

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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
2KE6_A	K10_TLS links to Rfam database...	0.89	0.84	0.94	16	1111	2	0	1	1	3
2KUR_A	K10_TLS links to Rfam database...	0.87	0.81	0.94	17	1110	1	0	1	0	4
2KUU_A	K10_TLS links to Rfam database...	0.84	0.76	0.94	16	1111	2	0	1	1	5
2KUV_A	K10_TLS links to Rfam database...	0.85	0.77	0.94	17	1110	1	0	1	0	5
2KUW_A	K10_TLS links to Rfam database...	0.76	0.67	0.88	14	1112	2	0	2	0	7
2KX8_A	7SK links to Rfam database...	-0.01	0.00	0.00	0	859	2	0	2	0	18
2L1F_B	Gammaretro_CES links to Rfam database...	0.96	0.92	1.00	23	2122	0	0	0	0	2
2L1F_A	Gammaretro_CES links to Rfam database...	0.91	0.88	0.95	21	2058	1	0	1	0	3
2L94_A	HIV_FE links to Rfam database...	0.57	0.55	0.61	11	972	7	0	7	0	9
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1530	12	0	10	2	20
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	11	5	3	3	7
2WWQ_V	tRNA links to Rfam database...	0.56	0.46	0.68	13	2907	7	0	6	1	15
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.59	0.55	0.65	11	4543	18	0	6	12	9
2XQD_Y	tRNA links to Rfam database...	0.77	0.67	0.90	18	2830	2	0	2	0	9
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.67	0.57	0.80	24	5121	7	0	6	1	18
2ZZM_B	tRNA links to Rfam database...	0.56	0.44	0.74	14	3467	5	4	1	0	18
2ZZN_D	tRNA links to Rfam database...	0.86	0.74	1.00	20	2465	0	0	0	0	7
3A2K_C	tRNA links to Rfam database...	0.84	0.71	1.00	20	2906	0	0	0	0	8
3A3A_A	tRNA-Sec links to Rfam database...	0.77	0.65	0.92	24	3629	3	0	2	1	13
3AKZ_H	tRNA links to Rfam database...	0.86	0.75	1.00	21	2680	0	0	0	0	7
3AMU_B	tRNA links to Rfam database...	0.84	0.70	1.00	19	2984	1	0	0	1	8
3GX2_A	SAM links to Rfam database...	0.70	0.60	0.83	24	4342	6	0	5	1	16
3IVN_B	Purine links to Rfam database...	0.65	0.45	0.93	14	2331	1	1	0	0	17
3IYQ_A	tmRNA links to Rfam database...	0.45	0.38	0.54	36	60659	37	4	27	6	58
3IZ4_A	tmRNA links to Rfam database...	0.69	0.55	0.88	72	70794	11	3	7	1	60
3IZF_C	5S_rRNA links to Rfam database...	0.67	0.57	0.79	31	6864	9	1	7	1	23
3J16_L	tRNA links to Rfam database...	0.82	0.67	1.00	20	2755	0	0	0	0	10
3JYV_7	tRNA links to Rfam database...	0.79	0.63	1.00	20	2830	0	0	0	0	12
3JYX_4	5_8S_rRNA links to Rfam database...	0.38	0.30	0.48	10	12225	21	3	8	10	23
3JYX_3	5S_rRNA links to Rfam database...	0.58	0.56	0.60	15	6303	21	1	9	11	12
3LA5_A	Purine links to Rfam database...	0.75	0.56	1.00	19	2466	0	0	0	0	15
3NPB_A	SAM links to Rfam database...	0.69	0.59	0.82	27	6988	9	2	4	3	19
3O58_2	5S_rRNA links to Rfam database...	0.79	0.79	0.79	30	7222	10	4	4	2	8
3O58_3	5_8S_rRNA links to Rfam database...	0.45	0.34	0.60	12	12383	19	2	6	11	23
3PDR_A	ykoK links to Rfam database...	0.73	0.63	0.87	45	12828	9	2	5	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...	0.63	0.55	0.74	23	3885	8	1	7	0	19
3UZL_B	tRNA links to Rfam database...	0.66	0.49	0.90	18	3550	2	1	1	0	19
4A1C_3	5S_rRNA links to Rfam database...	0.75	0.65	0.88	35	7100	5	1	4	0	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.35	0.24	0.50	8	11765	20	1	7	12	25
4AOB_A	SAM links to Rfam database...	0.66	0.55	0.79	23	4342	7	0	6	1	19
4ENB_A	crcB links to Rfam database...	0.48	0.32	0.75	6	1267	2	0	2	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	1	3	0	13

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Performance of CentroidAlifold(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	629
Total TN	296193
Total FP	122
Total FP CONTRA	14
Total FP INCONS	73
Total FP COMP	35
Total FN	873

Total Scores
MCC	0.605
Average MCC ± 95% Confidence Intervals	0.566 ± 0.067
Sensitivity	0.419
Positive Predictive Value	0.878
Nr of predictions	43

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KE6_A	K10_TLS links to Rfam database...	0.44	0.42	0.47	8	1111	10	0	9	1	11
2KUR_A	K10_TLS links to Rfam database...	0.77	0.71	0.83	15	1110	3	0	3	0	6
2KUU_A	K10_TLS links to Rfam database...	0.84	0.76	0.94	16	1111	2	0	1	1	5
2KUV_A	K10_TLS links to Rfam database...	0.44	0.41	0.50	9	1110	9	0	9	0	13
2KUW_A	K10_TLS links to Rfam database...	0.45	0.43	0.50	9	1110	9	0	9	0	12
2KX8_A	7SK links to Rfam database...	0.00	0.00	0.00	0	861	0	0	0	0	18
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L94_A	HIV_FE links to Rfam database...	0.53	0.50	0.59	10	973	7	0	7	0	10
2LC8_A	GP_knot1 links to Rfam database...	0.00	0.00	0.00	0	1540	0	0	0	0	20
2WRQ_Y	tRNA links to Rfam database...	0.24	0.12	0.50	2	2846	4	0	2	2	15
2WWQ_V	tRNA links to Rfam database...	0.46	0.21	1.00	6	2920	0	0	0	0	22
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.53	0.50	0.56	10	4542	20	0	8	12	10
2XQD_Y	tRNA links to Rfam database...	0.47	0.22	1.00	6	2844	0	0	0	0	21
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.77	0.64	0.93	27	5122	3	0	2	1	15
2ZZM_B	tRNA links to Rfam database...	0.14	0.06	0.33	2	3480	4	0	4	0	30
2ZZN_D	tRNA links to Rfam database...	0.47	0.22	1.00	6	2479	0	0	0	0	21
3A2K_C	tRNA links to Rfam database...	0.46	0.21	1.00	6	2920	0	0	0	0	22
3A3A_A	tRNA-Sec links to Rfam database...	0.85	0.73	1.00	27	3628	0	0	0	0	10
3AKZ_H	tRNA links to Rfam database...	0.46	0.21	1.00	6	2695	0	0	0	0	22
3AMU_B	tRNA links to Rfam database...	0.47	0.22	1.00	6	2997	0	0	0	0	21
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
3IYQ_A	tmRNA links to Rfam database...	0.52	0.39	0.70	37	60673	21	10	6	5	57
3IZ4_A	tmRNA links to Rfam database...	0.58	0.39	0.88	51	70818	7	2	5	0	81
3IZF_C	5S_rRNA links to Rfam database...	0.54	0.30	1.00	16	6887	0	0	0	0	38
3J16_L	tRNA links to Rfam database...	0.45	0.20	1.00	6	2769	0	0	0	0	24
3JYV_7	tRNA links to Rfam database...	0.43	0.19	1.00	6	2844	0	0	0	0	26
3JYX_4	5_8S_rRNA links to Rfam database...	0.52	0.30	0.91	10	12235	3	0	1	2	23
3JYX_3	5S_rRNA links to Rfam database...	0.59	0.41	0.85	11	6315	5	0	2	3	16
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...	0.71	0.54	0.93	25	6994	4	1	1	2	21
3O58_2	5S_rRNA links to Rfam database...	0.65	0.42	1.00	16	7244	0	0	0	0	22
3O58_3	5_8S_rRNA links to Rfam database...	0.56	0.34	0.92	12	12390	1	0	1	0	23
3PDR_A	ykoK links to Rfam database...	0.77	0.61	0.98	44	12835	3	0	1	2	28
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	0.52	0.96	22	3893	1	0	1	0	20
3UZL_B	tRNA links to Rfam database...	0.40	0.16	1.00	6	3564	0	0	0	0	31
4A1C_3	5S_rRNA links to Rfam database...	0.54	0.30	1.00	16	7124	0	0	0	0	38
4A1C_2	5_8S_rRNA links to Rfam database...	0.46	0.24	0.89	8	11772	3	0	1	2	25
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...	0.65	0.42	1.00	8	1267	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.65	0.42	1.00	8	1318	0	0	0	0	11

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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 CentroidAlifold(seed) - scored lower in this pairwise comparison

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

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