CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Pknots		RNAwolf
MCC	0.602	>	0.513
Average MCC ± 95% Confidence Intervals	0.656 ± 0.085	>	0.559 ± 0.092
Sensitivity	0.636	>	0.516
Positive Predictive Value	0.581	>	0.523
Total TP	725	>	588
Total TN	80920	<	81042
Total FP	660	<	676
Total FP CONTRA	151	>	138
Total FP INCONS	371	<	399
Total FP COMP	138	<	139
Total FN	415	<	552
P-value	3.56938820447e-08

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Performance plots

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

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Performance of Pknots - scored higher in this pairwise comparison

1. Total counts & total scores for Pknots

Total Base Pair Counts
Total TP	725
Total TN	80920
Total FP	660
Total FP CONTRA	151
Total FP INCONS	371
Total FP COMP	138
Total FN	415

Total Scores
MCC	0.602
Average MCC ± 95% Confidence Intervals	0.656 ± 0.085
Sensitivity	0.636
Positive Predictive Value	0.581
Nr of predictions	64

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.83	0.83	0.83	15	510	3	2	1	0	3
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	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	-	0.48	0.55	0.43	16	2403	23	9	12	2	13
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LU0_A	-	1.00	1.00	1.00	16	422	0	0	0	0	0
2LWK_A	-	0.38	0.27	0.60	3	202	3	0	2	1	8
2M58_A	-	0.60	0.58	0.64	7	533	4	1	3	0	5
2YIE_X	-	0.53	0.57	0.50	4	536	6	1	3	2	3
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
3AMU_B	tRNA links to Rfam database...	1.00	1.00	1.00	19	1138	3	0	0	3	0
3J0L_2	-	0.44	0.46	0.43	12	2222	23	1	15	7	14
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.35	0.36	0.36	4	400	8	3	4	1	7
3J0L_1	-	0.73	0.62	0.89	8	475	3	0	1	2	5
3J0L_h	-	0.67	0.66	0.70	21	2110	11	4	5	2	11
3J0L_7	-	0.38	0.50	0.31	5	503	12	3	8	1	5
3J0L_g	-	-0.02	0.00	0.00	0	171	5	3	2	0	2
3J16_L	tRNA links to Rfam database...	0.41	0.43	0.41	9	1137	13	1	12	0	12
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J2L_3	5S_rRNA links to Rfam database...	0.79	0.79	0.79	27	2986	12	1	6	5	7
3J3D_C	tRNA links to Rfam database...	0.46	0.53	0.42	10	944	14	5	9	0	9
3J3E_7	5S_rRNA links to Rfam database...	0.56	0.56	0.58	19	2708	16	2	12	2	15
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.13	0.09	2	2720	33	5	15	13	13
3J3F_7	5S_rRNA links to Rfam database...	0.32	0.33	0.32	12	2896	27	2	24	1	24
3J3F_8	5_8S_rRNA links to Rfam database...	0.42	0.53	0.33	10	4731	37	10	10	17	9
3J3V_B	5S_rRNA links to Rfam database...	0.58	0.63	0.55	17	2625	20	3	11	6	10
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	0	1	0	3
3SD1_A	THF links to Rfam database...	0.78	0.76	0.81	22	1506	5	1	4	0	7
3SIU_F	-	0.86	0.75	1.00	6	139	0	0	0	0	2
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	-	0.33	0.36	0.32	8	1251	17	4	13	0	14
3UZL_B	tRNA links to Rfam database...	1.00	1.00	1.00	16	1277	7	0	0	7	0
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.78	0.76	0.81	25	1958	7	1	5	1	8
3ZEX_F	-	0.00	0.00	0.00	0	910	12	0	4	8	4
3ZEX_C	5_8S_rRNA links to Rfam database...	0.10	0.14	0.08	4	5322	54	13	35	6	25
3ZEX_G	-	0.45	0.49	0.42	22	6455	39	9	21	9	23
3ZEX_H	-	0.26	0.37	0.19	7	3588	33	14	16	3	12
3ZEX_D	5S_rRNA links to Rfam database...	0.31	0.34	0.30	12	2756	28	5	23	0	23
3ZND_W	tRNA links to Rfam database...	0.24	0.38	0.16	3	1172	25	9	7	9	5
4A1C_3	5S_rRNA links to Rfam database...	0.28	0.30	0.28	11	2723	30	4	25	1	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.29	8	4488	36	9	11	16	12
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.19	0.21	0.21	6	1409	23	3	19	1	23
4ATO_G	-	0.36	0.43	0.33	3	211	6	6	0	0	4
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	2	0	0	2	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FNJ_A	-	-0.04	0.00	0.00	0	240	10	0	10	0	12
4FRG_B	AdoCbl-variant links to Rfam database...	0.55	0.50	0.63	12	1183	7	0	7	0	12
4FRN_A	AdoCbl-variant links to Rfam database...	0.57	0.54	0.63	15	1824	9	3	6	0	13
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0
4JF2_A	preQ1-II links to Rfam database...	0.92	1.00	0.86	24	1054	4	4	0	0	0
4JRC_A	-	0.94	0.94	0.94	16	605	1	1	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	588
Total TN	81042
Total FP	676
Total FP CONTRA	138
Total FP INCONS	399
Total FP COMP	139
Total FN	552

Total Scores
MCC	0.513
Average MCC ± 95% Confidence Intervals	0.559 ± 0.092
Sensitivity	0.516
Positive Predictive Value	0.523
Nr of predictions	64

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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
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
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
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
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
2YIE_X	-	-0.01	0.00	0.00	0	536	11	1	7	3	7
2YIE_Z	-	0.62	0.63	0.63	5	594	7	1	2	4	3
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	8	0	5	3	4
3J0L_2	-	0.14	0.15	0.15	4	2223	26	4	19	3	22
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.14	0.18	0.14	2	397	13	4	8	1	9
3J0L_1	-	0.68	0.54	0.88	7	476	5	0	1	4	6
3J0L_h	-	0.47	0.41	0.57	13	2117	12	1	9	2	19
3J0L_7	-	-0.02	0.00	0.00	0	509	10	1	9	0	10
3J0L_g	-	-0.02	0.00	0.00	0	171	7	4	1	2	2
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
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_7	5S_rRNA links to Rfam database...	0.57	0.56	0.59	19	2709	15	1	12	2	15
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2719	37	6	17	14	15
3J3F_7	5S_rRNA links to Rfam database...	0.27	0.28	0.28	10	2898	27	4	22	1	26
3J3F_8	5_8S_rRNA links to Rfam database...	0.28	0.37	0.23	7	4730	39	9	15	15	12
3J3V_B	5S_rRNA links to Rfam database...	0.59	0.59	0.59	16	2629	16	1	10	5	11
3RKF_A	Purine links to Rfam database...	0.89	0.83	0.95	20	845	1	0	1	0	4
3SD1_A	THF links to Rfam database...	0.58	0.59	0.59	17	1504	12	2	10	0	12
3SIU_F	-	0.86	0.75	1.00	6	139	0	0	0	0	2
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_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_G	-	0.20	0.20	0.21	9	6465	37	13	20	4	36
3ZEX_H	-	-0.01	0.00	0.00	0	3593	33	17	15	1	19
3ZEX_D	5S_rRNA links to Rfam database...	0.26	0.26	0.27	9	2763	24	8	16	0	26
3ZND_W	tRNA links to Rfam database...	0.67	0.75	0.60	6	1181	15	0	4	11	2
4A1C_3	5S_rRNA links to Rfam database...	0.32	0.30	0.35	11	2732	21	1	19	1	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.12	0.15	0.10	3	4487	38	12	14	12	17
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 Pknots - scored higher in this pairwise comparison

1. Total counts & total scores for Pknots

2. Individual counts for Pknots [ 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 ]