CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	PknotsRG		RNASLOpt
MCC	0.653	>	0.580
Average MCC ± 95% Confidence Intervals	0.714 ± 0.094	>	0.634 ± 0.104
Sensitivity	0.684	>	0.559
Positive Predictive Value	0.630	>	0.608
Total TP	638	>	522
Total TN	105798	<	105952
Total FP	503	>	429
Total FP CONTRA	122	>	114
Total FP INCONS	252	>	222
Total FP COMP	129	>	93
Total FN	295	<	411
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of PknotsRG and RNASLOpt. 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 PknotsRG and RNASLOpt).
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 PknotsRG and RNASLOpt).
Comparison of average Matthews Correlation Coefficients (MCCs) for PknotsRG and RNASLOpt. 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 PknotsRG and RNASLOpt).

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Performance of PknotsRG - scored higher in this pairwise comparison

1. Total counts & total scores for PknotsRG

Total Base Pair Counts
Total TP	638
Total TN	105798
Total FP	503
Total FP CONTRA	122
Total FP INCONS	252
Total FP COMP	129
Total FN	295

Total Scores
MCC	0.653
Average MCC ± 95% Confidence Intervals	0.714 ± 0.094
Sensitivity	0.684
Positive Predictive Value	0.630
Nr of predictions	47

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.66	0.61	0.73	11	513	4	2	2	0	7
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	7	123	3	0	0	3	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.81	0.86	0.76	25	2407	10	6	2	2	4
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	0.95	0.91	1.00	10	197	1	0	0	1	1
3J0L_a	-	0.18	0.18	0.22	2	402	8	3	4	1	9
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_7	-	0.38	0.50	0.31	5	503	12	3	8	1	5
3J0L_h	-	0.87	0.81	0.93	26	2112	4	1	1	2	6
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_1	-	0.83	0.77	0.91	10	473	4	0	1	3	3
3J0L_2	-	0.29	0.31	0.29	8	2222	27	2	18	7	18
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	0	0	0	0	4
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J20_0	tRNA links to Rfam database...	0.51	0.57	0.48	12	1194	14	3	10	1	9
3J2C_M	-	0.64	0.71	0.59	68	39809	75	20	28	27	28
3J2C_O	-	0.71	0.71	0.73	29	3947	17	2	9	6	12
3J2L_3	5S_rRNA links to Rfam database...	0.80	0.82	0.78	28	2984	12	1	7	4	6
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3TRZ_Z	-	1.00	1.00	1.00	5	87	1	0	0	1	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3UZL_B	tRNA links to Rfam database...	0.49	0.50	0.50	8	1277	15	0	8	7	8
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.64	0.64	0.66	21	1957	12	4	7	1	12
3ZEX_F	-	-0.01	0.00	0.00	0	908	11	2	4	5	4
3ZEX_G	-	0.70	0.71	0.70	32	6461	23	6	8	9	13
3ZEX_E	-	0.00	0.00	0.00	0	8254	55	17	33	5	34
3ZEX_D	5S_rRNA links to Rfam database...	0.88	0.83	0.94	29	2765	6	0	2	4	6
3ZEX_H	-	0.25	0.37	0.18	7	3586	32	20	12	0	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.30	0.34	0.26	10	5336	44	5	23	16	19
4A1C_3	5S_rRNA links to Rfam database...	0.85	0.84	0.86	31	2727	8	0	5	3	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4480	43	11	20	12	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ATO_G	-	0.88	1.00	0.78	7	211	2	2	0	0	0
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FNJ_A	-	0.91	0.83	1.00	10	240	0	0	0	0	2
4FRG_B	AdoCbl-variant links to Rfam database...	0.36	0.38	0.38	9	1178	15	2	13	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.59	0.57	0.62	16	1822	10	2	8	0	12
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0

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Performance of RNASLOpt - scored lower in this pairwise comparison

1. Total counts & total scores for RNASLOpt

Total Base Pair Counts
Total TP	522
Total TN	105952
Total FP	429
Total FP CONTRA	114
Total FP INCONS	222
Total FP COMP	93
Total FN	411

Total Scores
MCC	0.580
Average MCC ± 95% Confidence Intervals	0.634 ± 0.104
Sensitivity	0.559
Positive Predictive Value	0.608
Nr of predictions	47

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.48	0.39	0.64	7	517	4	0	4	0	11
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	7	123	3	0	0	3	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.70	0.69	0.71	20	2412	13	1	7	5	9
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	0.95	0.91	1.00	10	197	1	0	0	1	1
3J0L_a	-	0.21	0.18	0.29	2	404	6	3	2	1	9
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_7	-	-0.02	0.00	0.00	0	506	13	3	10	0	10
3J0L_h	-	0.81	0.66	1.00	21	2119	0	0	0	0	11
3J0L_8	-	0.74	0.57	1.00	4	72	0	0	0	0	3
3J0L_1	-	0.73	0.62	0.89	8	475	4	0	1	3	5
3J0L_2	-	0.49	0.46	0.52	12	2227	18	0	11	7	14
3J16_L	tRNA links to Rfam database...	0.63	0.57	0.71	12	1142	5	0	5	0	9
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	1	5
3J2C_M	-	0.46	0.49	0.44	47	39819	77	22	37	18	49
3J2C_O	-	0.72	0.68	0.76	28	3950	13	2	7	4	13
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.68	0.74	23	2989	11	0	8	3	11
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3TRZ_Z	-	1.00	1.00	1.00	5	87	2	0	0	2	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3UZL_B	tRNA links to Rfam database...	0.55	0.50	0.62	8	1280	9	1	4	4	8
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.90	0.85	0.97	28	1960	2	0	1	1	5
3ZEX_F	-	0.00	0.00	0.00	0	914	0	0	0	0	4
3ZEX_G	-	0.00	0.00	0.00	0	6507	0	0	0	0	45
3ZEX_E	-	0.00	0.00	0.00	0	8254	55	20	30	5	34
3ZEX_D	5S_rRNA links to Rfam database...	0.86	0.74	1.00	26	2770	4	0	0	4	9
3ZEX_H	-	0.27	0.37	0.21	7	3592	26	16	10	0	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.34	0.31	10	5342	36	8	14	14	19
4A1C_3	5S_rRNA links to Rfam database...	0.79	0.73	0.87	27	2732	5	0	4	1	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.30	0.40	0.24	8	4482	35	13	13	9	12
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.31	0.28	0.38	8	1416	13	3	10	0	21
4ATO_G	-	0.36	0.43	0.33	3	211	6	6	0	0	4
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FNJ_A	-	-0.05	0.00	0.00	0	239	11	0	11	0	12
4FRG_B	AdoCbl-variant links to Rfam database...	0.60	0.58	0.64	14	1180	8	3	5	0	10
4FRN_A	AdoCbl-variant links to Rfam database...	0.19	0.18	0.22	5	1825	18	6	12	0	23
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0

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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 PknotsRG - scored higher in this pairwise comparison

1. Total counts & total scores for PknotsRG

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

Performance of RNASLOpt - scored lower in this pairwise comparison

1. Total counts & total scores for RNASLOpt

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