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		Cylofold
MCC	0.661	>	0.648
Average MCC ± 95% Confidence Intervals	0.685 ± 0.072	>	0.676 ± 0.066
Sensitivity	0.597	>	0.559
Positive Predictive Value	0.739	<	0.758
Total TP	884	>	827
Total TN	155109	<	155215
Total FP	356	>	305
Total FP CONTRA	39	>	36
Total FP INCONS	274	>	228
Total FP COMP	43	>	41
Total FN	596	<	653
P-value	6.53888633552e-08

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Performance plots

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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	884
Total TN	155109
Total FP	356
Total FP CONTRA	39
Total FP INCONS	274
Total FP COMP	43
Total FN	596

Total Scores
MCC	0.661
Average MCC ± 95% Confidence Intervals	0.685 ± 0.072
Sensitivity	0.597
Positive Predictive Value	0.739
Nr of predictions	63

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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
2KRL_A	-	0.67	0.58	0.79	23	5122	9	2	4	3	17
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2KXM_A	-	-0.02	0.00	0.00	0	346	5	0	5	0	10
2KZL_A	-	0.59	0.53	0.67	10	1470	5	1	4	0	9
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L2K_A	-	0.94	0.89	1.00	17	844	0	0	0	0	2
2L3C_B	-	0.87	0.76	1.00	13	548	0	0	0	0	4
2L3E_A	-	0.96	0.92	1.00	12	583	1	0	0	1	1
2L3J_B	mir-2985-2 links to Rfam database...	0.94	0.88	1.00	30	2455	0	0	0	0	4
2L5Z_A	-	0.86	0.75	1.00	9	316	0	0	0	0	3
2L94_A	HIV_FE links to Rfam database...	0.92	0.90	0.95	18	971	1	0	1	0	2
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	0	14
2LC8_A	GP_knot1 links to Rfam database...	0.79	0.75	0.83	15	1522	3	1	2	0	5
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LDT_A	-	0.85	0.73	1.00	11	454	0	0	0	0	4
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.44	0.44	0.45	17	6067	22	4	17	1	22
2LWK_A	-	0.33	0.23	0.50	3	490	3	0	3	0	10
2RRC_A	-	0.77	0.60	1.00	6	225	0	0	0	0	4
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.23	0.25	0.22	5	4537	31	1	17	13	15
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.32	0.31	0.34	13	5113	25	1	24	0	29
2Y9C_V	-	0.59	0.50	0.71	12	2261	6	1	4	1	12
2YIE_Z	-	-0.01	0.00	0.00	0	1525	15	3	12	0	12
2YIE_X	-	0.36	0.33	0.40	4	1368	6	2	4	0	8
3ADB_C	-	0.92	0.84	1.00	32	4154	0	0	0	0	6
3AKZ_H	tRNA links to Rfam database...	0.84	0.75	0.95	21	2679	1	1	0	0	7
3AM1_B	-	0.91	0.83	1.00	29	3211	0	0	0	0	6
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	2	0	0	2	7
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.61	0.80	33	6862	8	1	7	0	21
3J0L_7	-	0.28	0.29	0.29	5	1208	12	0	12	0	12
3J0L_2	-	0.36	0.36	0.36	12	6183	23	3	18	2	21
3J0L_a	-	0.35	0.31	0.42	5	1116	7	1	6	0	11
3J0L_1	-	0.65	0.47	0.90	9	1215	2	0	1	1	10
3J0L_h	-	0.58	0.49	0.70	21	6075	11	0	9	2	22
3J0L_g	-	-0.01	0.00	0.00	0	460	5	2	3	0	4
3J16_L	tRNA links to Rfam database...	0.34	0.30	0.41	9	2753	13	0	13	0	21
3NDB_M	-	0.77	0.69	0.88	42	9132	7	1	5	1	19
3NKB_B	-	0.55	0.50	0.62	13	1995	8	0	8	0	13
3NMU_E	-	0.54	0.50	0.60	3	556	5	0	2	3	3
3O58_3	5_8S_rRNA links to Rfam database...	0.27	0.31	0.24	11	12357	38	11	24	3	24
3O58_2	5S_rRNA links to Rfam database...	0.83	0.74	0.93	28	7230	3	0	2	1	10
3OVB_D	-	1.00	1.00	1.00	11	584	1	0	0	1	0
3OVS_D	-	0.96	0.92	1.00	12	549	0	0	0	0	1
3P22_G	-	0.96	0.92	1.00	11	730	0	0	0	0	1
3PDR_A	ykoK links to Rfam database...	0.54	0.44	0.65	32	12831	19	0	17	2	40
3R4F_A	-	0.92	0.88	0.96	22	2122	1	0	1	0	3
3R9X_C	-	0.73	0.70	0.78	7	586	5	0	2	3	3
3RKF_A	Purine links to Rfam database...	0.77	0.62	0.95	21	2189	1	0	1	0	13
3SD1_A	THF links to Rfam database...	0.65	0.52	0.81	22	3889	5	0	5	0	20
3SIU_F	-	0.73	0.55	1.00	6	372	0	0	0	0	5
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	1	0	0	1	1
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3U4M_B	-	0.26	0.22	0.32	8	3135	17	0	17	0	29
3UZL_B	tRNA links to Rfam database...	0.75	0.59	0.96	22	3547	1	0	1	0	15
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.17	0.14	0.21	6	4343	23	1	21	1	36
4ENB_A	crcB links to Rfam database...	0.83	0.79	0.88	15	1258	2	1	1	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

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Performance of Cylofold - scored lower in this pairwise comparison

1. Total counts & total scores for Cylofold

Total Base Pair Counts
Total TP	827
Total TN	155215
Total FP	305
Total FP CONTRA	36
Total FP INCONS	228
Total FP COMP	41
Total FN	653

Total Scores
MCC	0.648
Average MCC ± 95% Confidence Intervals	0.676 ± 0.066
Sensitivity	0.559
Positive Predictive Value	0.758
Nr of predictions	63

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.72	0.60	0.86	24	5123	8	2	2	4	16
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2KXM_A	-	0.70	0.50	1.00	5	346	0	0	0	0	5
2KZL_A	-	0.72	0.53	1.00	10	1475	0	0	0	0	9
2L1F_A	Gammaretro_CES links to Rfam database...	0.91	0.83	1.00	20	2060	0	0	0	0	4
2L1F_B	Gammaretro_CES links to Rfam database...	0.92	0.84	1.00	21	2124	0	0	0	0	4
2L2K_A	-	0.82	0.68	1.00	13	848	0	0	0	0	6
2L3C_B	-	0.76	0.59	1.00	10	551	0	0	0	0	7
2L3E_A	-	0.96	0.92	1.00	12	583	1	0	0	1	1
2L3J_B	mir-2985-2 links to Rfam database...	0.89	0.79	1.00	27	2458	0	0	0	0	7
2L5Z_A	-	0.86	0.75	1.00	9	316	0	0	0	0	3
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	0	14
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	5	0	5	0	9
2LDL_A	-	0.73	0.55	1.00	6	345	0	0	0	0	5
2LDT_A	-	0.85	0.73	1.00	11	454	0	0	0	0	4
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.50	0.44	0.59	17	6076	12	2	10	0	22
2LWK_A	-	0.83	0.77	0.91	10	485	1	0	1	0	3
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.38	0.40	0.36	8	4538	23	7	7	9	12
2XQD_Y	tRNA links to Rfam database...	0.81	0.78	0.84	21	2825	4	4	0	0	6
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.10	0.10	0.11	4	5115	32	1	31	0	38
2Y9C_V	-	0.59	0.54	0.65	13	2258	8	1	6	1	11
2YIE_Z	-	-0.01	0.00	0.00	0	1529	11	3	8	0	12
2YIE_X	-	0.30	0.33	0.29	4	1364	10	2	8	0	8
3ADB_C	-	0.78	0.71	0.87	27	4155	4	0	4	0	11
3AKZ_H	tRNA links to Rfam database...	0.66	0.57	0.76	16	2680	6	0	5	1	12
3AM1_B	-	0.76	0.63	0.92	22	3216	2	0	2	0	13
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	6867	6	0	6	0	24
3J0L_7	-	0.30	0.29	0.33	5	1210	10	0	10	0	12
3J0L_2	-	0.39	0.36	0.43	12	6188	18	2	14	2	21
3J0L_a	-	0.22	0.19	0.27	3	1117	8	1	7	0	13
3J0L_1	-	0.65	0.47	0.90	9	1215	2	0	1	1	10
3J0L_h	-	0.48	0.37	0.62	16	6079	10	0	10	0	27
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3NDB_M	-	0.58	0.48	0.71	29	9139	13	1	11	1	32
3NKB_B	-	0.40	0.31	0.53	8	2001	7	0	7	0	18
3NMU_E	-	0.20	0.17	0.25	1	557	6	1	2	3	5
3O58_3	5_8S_rRNA links to Rfam database...	0.36	0.34	0.38	12	12371	29	5	15	9	23
3O58_2	5S_rRNA links to Rfam database...	0.80	0.68	0.93	26	7232	3	0	2	1	12
3OVB_D	-	1.00	1.00	1.00	11	584	1	0	0	1	0
3OVS_D	-	0.96	0.92	1.00	12	549	0	0	0	0	1
3P22_G	-	0.96	0.92	1.00	11	730	0	0	0	0	1
3PDR_A	ykoK links to Rfam database...	0.72	0.54	0.95	39	12839	4	0	2	2	33
3R4F_A	-	0.96	0.92	1.00	23	2122	0	0	0	0	2
3R9X_C	-	0.84	0.80	0.89	8	586	2	0	1	1	2
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...	0.62	0.50	0.78	21	3889	6	0	6	0	21
3SIU_F	-	0.73	0.55	1.00	6	372	0	0	0	0	5
3SN2_B	IRE_II links to Rfam database...	0.64	0.42	1.00	5	401	0	0	0	0	7
3TRZ_Z	-	0.91	0.83	1.00	5	205	1	0	0	1	1
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...	0.45	0.38	0.54	14	3544	12	1	11	0	23
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

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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 Cylofold - scored lower in this pairwise comparison

1. Total counts & total scores for Cylofold

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