CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Fold		RNASLOpt
MCC	0.496	>	0.489
Average MCC ± 95% Confidence Intervals	0.603 ± 0.103	>	0.580 ± 0.099
Sensitivity	0.438	>	0.393
Positive Predictive Value	0.567	<	0.614
Total TP	624	>	559
Total TN	280071	<	280261
Total FP	525	>	392
Total FP CONTRA	45	>	43
Total FP INCONS	432	>	309
Total FP COMP	48	>	40
Total FN	800	<	865
P-value	2.29562105844e-05

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Performance plots

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

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Performance of Fold - scored higher in this pairwise comparison

1. Total counts & total scores for Fold

Total Base Pair Counts
Total TP	624
Total TN	280071
Total FP	525
Total FP CONTRA	45
Total FP INCONS	432
Total FP COMP	48
Total FN	800

Total Scores
MCC	0.496
Average MCC ± 95% Confidence Intervals	0.603 ± 0.103
Sensitivity	0.438
Positive Predictive Value	0.567
Nr of predictions	47

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2. Individual counts for Fold [ 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...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LHP_A	-	0.97	0.94	1.00	15	651	0	0	0	0	1
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LJJ_A	-	1.00	1.00	1.00	8	343	2	0	0	2	0
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.85	0.79	0.91	31	6071	5	0	3	2	8
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LWK_A	-	0.96	0.92	1.00	12	484	0	0	0	0	1
3J0L_a	-	0.20	0.19	0.23	3	1115	10	2	8	0	13
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_7	-	-0.01	0.00	0.00	0	1213	12	0	12	0	17
3J0L_h	-	0.81	0.65	1.00	28	6077	2	0	0	2	15
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_1	-	0.76	0.63	0.92	12	1212	2	0	1	1	7
3J0L_2	-	0.25	0.24	0.26	8	6185	25	2	21	2	25
3J16_L	tRNA links to Rfam database...	0.63	0.53	0.76	16	2754	5	0	5	0	14
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...	0.45	0.40	0.52	12	2827	12	0	11	1	18
3J2C_M	-	0.19	0.15	0.23	32	106350	110	5	104	1	175
3J2C_O	-	0.59	0.54	0.65	34	10244	18	1	17	0	29
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.53	0.74	28	7837	12	0	10	2	25
3SN2_B	IRE_II links to Rfam database...	1.00	1.00	1.00	12	394	0	0	0	0	0
3TRZ_Z	-	0.91	0.83	1.00	5	205	1	0	0	1	1
3TS0_U	-	1.00	1.00	1.00	6	247	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3U4M_B	-	0.45	0.35	0.59	13	3138	9	1	8	0	24
3UZL_B	tRNA links to Rfam database...	0.77	0.62	0.96	23	3546	1	0	1	0	14
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.85	0.75	0.97	30	4722	2	0	1	1	10
3ZEX_F	-	0.00	0.00	0.00	0	2617	11	2	9	0	12
3ZEX_G	-	0.76	0.65	0.89	48	16417	12	0	6	6	26
3ZEX_E	-	0.00	0.00	0.00	0	21890	57	2	53	2	77
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.67	0.87	33	6983	5	1	4	0	16
3ZEX_H	-	0.18	0.18	0.19	7	9008	30	5	25	0	31
3ZEX_C	5_8S_rRNA links to Rfam database...	0.22	0.21	0.24	11	14151	45	4	30	11	41
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.57	0.82	31	7102	7	1	6	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11744	43	5	27	11	28
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ATO_G	-	0.32	0.30	0.38	3	520	5	1	4	0	7
4ENB_A	crcB links to Rfam database...	0.32	0.26	0.42	5	1263	7	1	6	0	14
4ENC_A	crcB links to Rfam database...	0.31	0.26	0.38	5	1313	8	1	7	0	14
4FNJ_A	-	0.79	0.63	1.00	10	585	0	0	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.24	0.22	0.27	7	3460	19	3	16	0	25
4FRN_A	AdoCbl-variant links to Rfam database...	0.41	0.36	0.46	13	5123	15	2	13	0	23
4HXH_A	-	1.00	1.00	1.00	6	319	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	559
Total TN	280261
Total FP	392
Total FP CONTRA	43
Total FP INCONS	309
Total FP COMP	40
Total FN	865

Total Scores
MCC	0.489
Average MCC ± 95% Confidence Intervals	0.580 ± 0.099
Sensitivity	0.393
Positive Predictive Value	0.614
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...	0.47	0.35	0.64	7	1529	4	0	4	0	13
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LHP_A	-	0.97	0.94	1.00	15	651	0	0	0	0	1
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LJJ_A	-	1.00	1.00	1.00	8	343	2	0	0	2	0
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.68	0.62	0.75	24	6073	9	0	8	1	15
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LWK_A	-	0.83	0.77	0.91	10	485	1	0	1	0	3
3J0L_a	-	0.26	0.19	0.38	3	1120	5	1	4	0	13
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_h	-	0.70	0.49	1.00	21	6084	0	0	0	0	22
3J0L_8	-	0.70	0.50	1.00	4	186	0	0	0	0	4
3J0L_1	-	0.65	0.47	0.90	9	1215	3	0	1	2	10
3J0L_2	-	0.39	0.36	0.43	12	6188	18	2	14	2	21
3J16_L	tRNA links to Rfam database...	0.53	0.40	0.71	12	2758	5	0	5	0	18
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...	0.66	0.57	0.77	17	2828	6	1	4	1	13
3J2C_M	-	0.38	0.29	0.50	60	106370	64	11	50	3	147
3J2C_O	-	0.62	0.49	0.78	31	10256	10	0	9	1	32
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.43	0.72	23	7843	11	0	9	2	30
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3TRZ_Z	-	0.91	0.83	1.00	5	205	2	0	0	2	1
3TS0_U	-	1.00	1.00	1.00	6	247	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.48	0.32	0.71	12	3553	5	0	5	0	25
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.82	0.70	0.97	28	4724	2	0	1	1	12
3ZEX_F	-	0.00	0.00	0.00	0	2628	0	0	0	0	12
3ZEX_G	-	0.00	0.00	0.00	0	16471	0	0	0	0	74
3ZEX_E	-	0.00	0.00	0.00	0	21892	55	4	49	2	77
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.59	0.97	29	6991	1	0	1	0	20
3ZEX_H	-	0.19	0.18	0.21	7	9012	26	4	22	0	31
3ZEX_C	5_8S_rRNA links to Rfam database...	0.26	0.21	0.33	11	14163	35	2	20	13	41
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.24	0.22	8	11744	35	8	21	6	25
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.26	0.19	0.38	8	4350	13	2	11	0	34
4ATO_G	-	0.30	0.30	0.33	3	519	6	2	4	0	7
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10
4FNJ_A	-	-0.02	0.00	0.00	0	584	11	0	11	0	16
4FRG_B	AdoCbl-variant links to Rfam database...	0.56	0.47	0.68	15	3464	7	1	6	0	17
4FRN_A	AdoCbl-variant links to Rfam database...	0.20	0.17	0.26	6	5128	17	2	15	0	30
4HXH_A	-	1.00	1.00	1.00	6	319	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 Fold - scored higher in this pairwise comparison

1. Total counts & total scores for Fold

2. Individual counts for Fold [ 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 ]