CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNASLOpt		RNAwolf
MCC	0.582	>	0.441
Average MCC ± 95% Confidence Intervals	0.624 ± 0.091	>	0.520 ± 0.096
Sensitivity	0.568	>	0.455
Positive Predictive Value	0.605	>	0.437
Total TP	676	>	542
Total TN	128049	>	127926
Total FP	580	<	840
Total FP CONTRA	151	<	199
Total FP INCONS	291	<	500
Total FP COMP	138	<	141
Total FN	515	<	649
P-value	3.56938820447e-08

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Performance plots

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

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Performance of RNASLOpt - scored higher in this pairwise comparison

1. Total counts & total scores for RNASLOpt

Total Base Pair Counts
Total TP	676
Total TN	128049
Total FP	580
Total FP CONTRA	151
Total FP INCONS	291
Total FP COMP	138
Total FN	515

Total Scores
MCC	0.582
Average MCC ± 95% Confidence Intervals	0.624 ± 0.091
Sensitivity	0.568
Positive Predictive Value	0.605
Nr of predictions	59

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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
2LU0_A	-	0.93	0.88	1.00	14	424	0	0	0	0	2
2LWK_A	-	0.95	0.91	1.00	10	197	1	0	0	1	1
2M58_A	-	0.37	0.33	0.44	4	535	5	4	1	0	8
3J0L_a	-	0.21	0.18	0.29	2	404	6	3	2	1	9
3J0L_2	-	0.49	0.46	0.52	12	2227	18	0	11	7	14
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_1	-	0.73	0.62	0.89	8	475	4	0	1	3	5
3J0L_8	-	0.74	0.57	1.00	4	72	0	0	0	0	3
3J16_L	tRNA links to Rfam database...	0.63	0.57	0.71	12	1142	5	0	5	0	9
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	1	5
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J2C_O	-	0.72	0.68	0.76	28	3950	13	2	7	4	13
3J2C_M	-	0.46	0.49	0.44	47	39819	77	22	37	18	49
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.68	0.74	23	2989	11	0	8	3	11
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	3	3	0	0	1
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2724	30	6	12	12	15
3J3E_7	5S_rRNA links to Rfam database...	0.61	0.56	0.68	19	2713	10	1	8	1	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.47	0.32	9	4733	38	10	9	19	10
3J3F_7	5S_rRNA links to Rfam database...	0.21	0.22	0.22	8	2898	28	3	25	0	28
3J3V_B	5S_rRNA links to Rfam database...	0.60	0.59	0.62	16	2630	14	2	8	4	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
3W1K_J	tRNA-Sec links to Rfam database...	0.93	0.90	0.97	28	1649	1	1	0	0	3
3W3S_B	tRNA-Sec links to Rfam database...	0.90	0.85	0.97	28	1960	2	0	1	1	5
3ZEX_H	-	0.27	0.37	0.21	7	3592	26	16	10	0	12
3ZEX_F	-	0.00	0.00	0.00	0	914	0	0	0	0	4
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.34	0.31	10	5342	36	8	14	14	19
3ZEX_D	5S_rRNA links to Rfam database...	0.86	0.74	1.00	26	2770	4	0	0	4	9
3ZEX_E	-	0.00	0.00	0.00	0	8254	55	20	30	5	34
3ZEX_G	-	0.00	0.00	0.00	0	6507	0	0	0	0	45
3ZND_W	tRNA links to Rfam database...	0.26	0.38	0.19	3	1175	22	7	6	9	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.30	0.40	0.24	8	4482	35	13	13	9	12
4A1C_3	5S_rRNA links to Rfam database...	0.79	0.73	0.87	27	2732	5	0	4	1	10
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
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5
4JRC_A	-	0.97	0.94	1.00	16	606	0	0	0	0	1

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Performance of RNAwolf - scored lower in this pairwise comparison

1. Total counts & total scores for RNAwolf

Total Base Pair Counts
Total TP	542
Total TN	127926
Total FP	840
Total FP CONTRA	199
Total FP INCONS	500
Total FP COMP	141
Total FN	649

Total Scores
MCC	0.441
Average MCC ± 95% Confidence Intervals	0.520 ± 0.096
Sensitivity	0.455
Positive Predictive Value	0.437
Nr of predictions	59

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2. Individual counts for RNAwolf [ 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...	0.52	0.50	0.56	9	512	7	0	7	0	9
2LDL_A	-	0.88	0.78	1.00	7	133	0	0	0	0	2
2LHP_A	-	1.00	1.00	1.00	15	246	1	0	0	1	0
2LI4_A	-	0.96	0.93	1.00	13	176	0	0	0	0	1
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	-	0.84	0.79	0.88	23	2414	11	0	3	8	6
2LQZ_A	-	1.00	1.00	1.00	8	124	1	0	0	1	0
2LU0_A	-	0.97	0.94	1.00	15	423	0	0	0	0	1
2LWK_A	-	0.48	0.45	0.56	5	198	5	0	4	1	6
2M58_A	-	0.60	0.58	0.64	7	533	4	1	3	0	5
3J0L_a	-	0.14	0.18	0.14	2	397	13	4	8	1	9
3J0L_2	-	0.14	0.15	0.15	4	2223	26	4	19	3	22
3J0L_g	-	-0.02	0.00	0.00	0	171	7	4	1	2	2
3J0L_7	-	-0.02	0.00	0.00	0	509	10	1	9	0	10
3J0L_h	-	0.47	0.41	0.57	13	2117	12	1	9	2	19
3J0L_1	-	0.68	0.54	0.88	7	476	5	0	1	4	6
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J16_L	tRNA links to Rfam database...	0.58	0.57	0.60	12	1139	9	2	6	1	9
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	2	9	1	9
3J20_1	tRNA links to Rfam database...	0.53	0.55	0.52	11	1091	11	4	6	1	9
3J2C_O	-	0.41	0.44	0.40	18	3942	30	7	20	3	23
3J2C_M	-	0.21	0.25	0.19	24	39797	113	35	69	9	72
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.71	0.73	24	2987	13	1	8	4	10
3J3D_C	tRNA links to Rfam database...	0.92	0.95	0.90	18	948	3	2	0	1	1
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2719	37	6	17	14	15
3J3E_7	5S_rRNA links to Rfam database...	0.57	0.56	0.59	19	2709	15	1	12	2	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.28	0.37	0.23	7	4730	39	9	15	15	12
3J3F_7	5S_rRNA links to Rfam database...	0.27	0.28	0.28	10	2898	27	4	22	1	26
3J3V_B	5S_rRNA links to Rfam database...	0.59	0.59	0.59	16	2629	16	1	10	5	11
3SN2_B	IRE_II links to Rfam database...	1.00	1.00	1.00	12	142	0	0	0	0	0
3TRZ_Z	-	1.00	1.00	1.00	5	87	0	0	0	0	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	-0.05	0.00	0.00	0	103	6	0	5	1	5
3U4M_B	-	0.50	0.50	0.52	11	1255	12	1	9	2	11
3UZL_B	tRNA links to Rfam database...	0.93	0.88	1.00	14	1279	7	0	0	7	2
3VJR_D	-	1.00	1.00	1.00	12	239	1	0	0	1	0
3W1K_J	tRNA-Sec links to Rfam database...	0.81	0.77	0.86	24	1650	5	0	4	1	7
3W3S_B	tRNA-Sec links to Rfam database...	0.70	0.70	0.72	23	1957	10	0	9	1	10
3ZEX_H	-	-0.01	0.00	0.00	0	3593	33	17	15	1	19
3ZEX_F	-	0.00	0.00	0.00	0	910	17	0	4	13	4
3ZEX_C	5_8S_rRNA links to Rfam database...	0.08	0.10	0.07	3	5328	43	18	25	0	26
3ZEX_D	5S_rRNA links to Rfam database...	0.26	0.26	0.27	9	2763	24	8	16	0	26
3ZEX_E	-	-0.01	0.00	0.00	0	8244	60	23	37	0	34
3ZEX_G	-	0.20	0.20	0.21	9	6465	37	13	20	4	36
3ZND_W	tRNA links to Rfam database...	0.67	0.75	0.60	6	1181	15	0	4	11	2
4A1C_2	5_8S_rRNA links to Rfam database...	0.12	0.15	0.10	3	4487	38	12	14	12	17
4A1C_3	5S_rRNA links to Rfam database...	0.32	0.30	0.35	11	2732	21	1	19	1	26
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.26	0.24	0.30	7	1414	17	2	14	1	22
4ATO_G	-	-0.03	0.00	0.00	0	213	7	4	3	0	7
4ENB_A	crcB links to Rfam database...	0.45	0.40	0.55	6	461	5	1	4	0	9
4ENC_A	crcB links to Rfam database...	0.34	0.33	0.38	5	483	9	0	8	1	10
4FNJ_A	-	-0.04	0.00	0.00	0	243	7	0	7	0	12
4FRG_B	AdoCbl-variant links to Rfam database...	0.54	0.50	0.60	12	1182	8	3	5	0	12
4FRN_A	AdoCbl-variant links to Rfam database...	-0.01	0.00	0.00	0	1828	20	1	19	0	28
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0
4JF2_A	preQ1-II links to Rfam database...	0.72	0.67	0.80	16	1062	4	4	0	0	8
4JRC_A	-	0.71	0.65	0.79	11	608	3	2	1	0	6

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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 RNASLOpt - scored higher in this pairwise comparison

1. Total counts & total scores for RNASLOpt

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

Performance of RNAwolf - scored lower in this pairwise comparison

1. Total counts & total scores for RNAwolf

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