CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	MaxExpect		PknotsRG
MCC	0.617	>	0.559
Average MCC ± 95% Confidence Intervals	0.692 ± 0.059	<	0.701 ± 0.054
Sensitivity	0.540	>	0.499
Positive Predictive Value	0.705	>	0.628
Total TP	1997	>	1846
Total TN	4426793	>	4426685
Total FP	959	<	1204
Total FP CONTRA	92	<	116
Total FP INCONS	743	<	978
Total FP COMP	124	>	110
Total FN	1704	<	1855
P-value	3.56938820447e-08

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Performance plots

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Performance of MaxExpect - scored higher in this pairwise comparison

1. Total counts & total scores for MaxExpect

Total Base Pair Counts
Total TP	1997
Total TN	4426793
Total FP	959
Total FP CONTRA	92
Total FP INCONS	743
Total FP COMP	124
Total FN	1704

Total Scores
MCC	0.617
Average MCC ± 95% Confidence Intervals	0.692 ± 0.059
Sensitivity	0.540
Positive Predictive Value	0.705
Nr of predictions	99

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KD8_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	0.92	0.89	0.94	17	1110	2	0	1	1	2
2KPV_A	-	0.96	0.92	1.00	12	549	0	0	0	0	1
2KRL_A	-	0.76	0.60	0.96	24	5126	5	0	1	4	16
2KU0_A	-	-0.02	0.00	0.00	0	694	9	0	9	0	16
2KUR_A	K10_TLS links to Rfam database...	0.90	0.86	0.95	18	1109	1	0	1	0	3
2KUU_A	K10_TLS links to Rfam database...	0.87	0.81	0.94	17	1110	2	0	1	1	4
2KUV_A	K10_TLS links to Rfam database...	0.88	0.82	0.95	18	1109	1	0	1	0	4
2KUW_A	K10_TLS links to Rfam database...	0.90	0.86	0.95	18	1109	1	0	1	0	3
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2KXM_A	-	0.83	0.70	1.00	7	344	0	0	0	0	3
2KZL_A	-	0.86	0.74	1.00	14	1471	0	0	0	0	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L2K_A	-	0.94	0.89	1.00	17	844	0	0	0	0	2
2L3C_B	-	0.91	0.82	1.00	14	547	0	0	0	0	3
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...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LA5_A	-	0.39	0.26	0.63	5	622	3	1	2	0	14
2LBS_A	-	1.00	1.00	1.00	14	482	0	0	0	0	0
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
2LDT_A	-	0.85	0.73	1.00	11	454	0	0	0	0	4
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	-	0.81	0.74	0.88	29	6072	6	0	4	2	10
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LWK_A	-	0.88	0.85	0.92	11	484	1	0	1	0	2
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
2WRQ_Y	tRNA links to Rfam database...	0.53	0.53	0.53	9	2833	13	5	3	5	8
2WW9_D	-	0.14	0.12	0.19	3	1937	13	0	13	0	23
2WW9_F	-	0.69	0.70	0.70	7	290	3	0	3	0	3
2WW9_E	-	-0.01	0.00	0.00	0	556	5	0	5	0	14
2WWQ_V	tRNA links to Rfam database...	0.76	0.64	0.90	18	2906	3	0	2	1	10
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.51	0.50	0.53	10	4541	24	0	9	15	10
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...	0.25	0.24	0.27	10	5114	27	1	26	0	32
2Y8W_B	-	1.00	1.00	1.00	6	184	1	0	0	1	0
2Y9C_V	-	0.65	0.63	0.68	15	2256	8	1	6	1	9
2YIE_X	-	0.36	0.33	0.40	4	1368	6	2	4	0	8
2YIE_Z	-	-0.01	0.00	0.00	0	1525	15	3	12	0	12
3A2K_C	tRNA links to Rfam database...	0.42	0.39	0.46	11	2902	13	2	11	0	17
3ADB_C	-	0.80	0.74	0.88	28	4154	4	0	4	0	10
3AKZ_H	tRNA links to Rfam database...	0.84	0.75	0.95	21	2679	1	1	0	0	7
3AM1_B	-	0.78	0.71	0.86	25	3211	4	0	4	0	10
3AMU_B	tRNA links to Rfam database...	0.64	0.59	0.70	16	2980	9	0	7	2	11
3GX2_A	SAM links to Rfam database...	0.77	0.63	0.96	25	4345	2	0	1	1	15
3IAB_R	-	0.92	0.86	1.00	12	1023	0	0	0	0	2
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IWN_A	c-di-GMP-I links to Rfam database...	0.74	0.67	0.81	22	4251	6	0	5	1	11
3IYQ_A	tmRNA links to Rfam database...	0.29	0.31	0.27	29	60617	84	19	61	4	65
3IZ4_A	tmRNA links to Rfam database...	0.54	0.46	0.64	61	70781	39	3	31	5	71
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.61	0.83	33	6863	7	1	6	0	21
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_a	-	0.39	0.31	0.50	5	1118	5	2	3	0	11
3J0L_1	-	0.76	0.63	0.92	12	1212	2	0	1	1	7
3J0L_h	-	0.81	0.65	1.00	28	6077	2	0	0	2	15
3J0L_7	-	-0.01	0.00	0.00	0	1213	12	0	12	0	17
3J0L_2	-	0.25	0.24	0.26	8	6185	25	2	21	2	25
3J16_L	tRNA links to Rfam database...	0.29	0.23	0.37	7	2756	12	0	12	0	23
3JYV_7	tRNA links to Rfam database...	0.41	0.31	0.56	10	2832	8	0	8	0	22
3JYX_3	5S_rRNA links to Rfam database...	0.64	0.63	0.65	17	6302	19	1	8	10	10
3JYX_4	5_8S_rRNA links to Rfam database...	0.31	0.30	0.31	10	12214	34	4	18	12	23
3KIY_A	-	0.54	0.45	0.65	553	4053271	314	23	281	10	688
3KTW_C	-	0.54	0.47	0.65	20	4529	12	2	9	1	23
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NDB_M	-	0.78	0.69	0.89	42	9133	6	0	5	1	19
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3NMU_E	-	-0.01	0.00	0.00	0	553	10	1	7	2	6
3NPB_A	SAM links to Rfam database...	0.71	0.61	0.82	28	6987	9	0	6	3	18
3O58_2	5S_rRNA links to Rfam database...	0.75	0.76	0.74	29	7221	11	3	7	1	9
3O58_3	5_8S_rRNA links to Rfam database...	0.35	0.34	0.35	12	12369	35	2	20	13	23
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...	0.76	0.63	0.94	45	12832	5	0	3	2	27
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...	0.58	0.48	0.71	20	3888	8	1	7	0	22
3SIU_F	-	0.85	0.73	1.00	8	370	0	0	0	0	3
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
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	0	6	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11746	41	4	26	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
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...	0.31	0.26	0.38	5	1313	8	1	7	0	14

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Performance of PknotsRG - scored lower in this pairwise comparison

1. Total counts & total scores for PknotsRG

Total Base Pair Counts
Total TP	1846
Total TN	4426685
Total FP	1204
Total FP CONTRA	116
Total FP INCONS	978
Total FP COMP	110
Total FN	1855

Total Scores
MCC	0.559
Average MCC ± 95% Confidence Intervals	0.701 ± 0.054
Sensitivity	0.499
Positive Predictive Value	0.628
Nr of predictions	99

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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
2KD8_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	0.86	0.84	0.89	16	1110	3	0	2	1	3
2KPV_A	-	0.96	0.92	1.00	12	549	0	0	0	0	1
2KRL_A	-	0.72	0.60	0.86	24	5123	8	2	2	4	16
2KU0_A	-	0.83	0.69	1.00	11	692	0	0	0	0	5
2KUR_A	K10_TLS links to Rfam database...	0.85	0.81	0.89	17	1109	2	0	2	0	4
2KUU_A	K10_TLS links to Rfam database...	0.82	0.76	0.89	16	1110	3	0	2	1	5
2KUV_A	K10_TLS links to Rfam database...	0.83	0.77	0.89	17	1109	2	0	2	0	5
2KUW_A	K10_TLS links to Rfam database...	0.90	0.86	0.95	18	1109	1	0	1	0	3
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2KXM_A	-	0.83	0.70	1.00	7	344	0	0	0	0	3
2KZL_A	-	0.86	0.74	1.00	14	1471	0	0	0	0	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L2K_A	-	0.94	0.89	1.00	17	844	0	0	0	0	2
2L3C_B	-	0.91	0.82	1.00	14	547	0	0	0	0	3
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...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LA5_A	-	0.39	0.26	0.63	5	622	3	1	2	0	14
2LBS_A	-	1.00	1.00	1.00	14	482	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.63	0.55	0.73	11	1525	4	1	3	0	9
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
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	-	0.73	0.69	0.77	27	6070	8	2	6	0	12
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
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
2WRQ_Y	tRNA links to Rfam database...	0.53	0.53	0.53	9	2833	13	5	3	5	8
2WW9_D	-	0.14	0.12	0.19	3	1937	13	0	13	0	23
2WW9_F	-	0.69	0.70	0.70	7	290	3	0	3	0	3
2WW9_E	-	0.53	0.29	1.00	4	557	0	0	0	0	10
2WWQ_V	tRNA links to Rfam database...	0.76	0.68	0.86	19	2904	5	0	3	2	9
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.51	0.50	0.53	10	4541	22	0	9	13	10
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...	0.34	0.31	0.39	13	5118	20	1	19	0	29
2Y8W_B	-	1.00	1.00	1.00	6	184	1	0	0	1	0
2Y9C_V	-	0.66	0.63	0.71	15	2257	8	1	5	2	9
2YIE_X	-	0.30	0.33	0.29	4	1364	10	2	8	0	8
2YIE_Z	-	-0.01	0.00	0.00	0	1525	15	3	12	0	12
3A2K_C	tRNA links to Rfam database...	0.42	0.39	0.46	11	2902	13	2	11	0	17
3ADB_C	-	0.33	0.32	0.36	12	4153	21	0	21	0	26
3AKZ_H	tRNA links to Rfam database...	0.41	0.39	0.44	11	2676	14	4	10	0	17
3AM1_B	-	0.68	0.63	0.73	22	3210	8	1	7	0	13
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3GX2_A	SAM links to Rfam database...	0.67	0.55	0.81	22	4344	6	0	5	1	18
3IAB_R	-	0.92	0.86	1.00	12	1023	0	0	0	0	2
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IWN_A	c-di-GMP-I links to Rfam database...	0.20	0.18	0.24	6	4253	19	1	18	0	27
3IYQ_A	tmRNA links to Rfam database...	0.31	0.33	0.28	31	60617	80	24	54	2	63
3IZ4_A	tmRNA links to Rfam database...	0.51	0.47	0.55	62	70763	52	10	41	1	70
3IZF_C	5S_rRNA links to Rfam database...	0.59	0.52	0.67	28	6861	14	1	13	0	26
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_a	-	0.23	0.19	0.30	3	1118	7	1	6	0	13
3J0L_1	-	0.76	0.63	0.92	12	1212	2	0	1	1	7
3J0L_h	-	0.75	0.60	0.93	26	6077	4	0	2	2	17
3J0L_7	-	0.28	0.29	0.29	5	1208	12	0	12	0	12
3J0L_2	-	0.24	0.24	0.24	8	6183	27	2	23	2	25
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2828	22	1	21	0	32
3JYX_3	5S_rRNA links to Rfam database...	0.62	0.63	0.61	17	6300	22	1	10	11	10
3JYX_4	5_8S_rRNA links to Rfam database...	0.31	0.30	0.32	10	12215	33	5	16	12	23
3KIY_A	-	0.39	0.33	0.45	413	4053217	505	24	474	7	828
3KTW_C	-	0.77	0.65	0.90	28	4529	4	2	1	1	15
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NDB_M	-	0.77	0.69	0.86	42	9131	8	0	7	1	19
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3NMU_E	-	0.54	0.50	0.60	3	556	5	0	2	3	3
3NPB_A	SAM links to Rfam database...	0.83	0.72	0.97	33	6987	3	0	1	2	13
3O58_2	5S_rRNA links to Rfam database...	0.59	0.61	0.58	23	7220	19	4	13	2	15
3O58_3	5_8S_rRNA links to Rfam database...	0.34	0.34	0.34	12	12368	34	2	21	11	23
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...	0.75	0.63	0.90	45	12830	7	1	4	2	27
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...	0.61	0.50	0.75	21	3888	7	1	6	0	21
3SIU_F	-	0.85	0.73	1.00	8	370	0	0	0	0	3
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
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	0.38	0.61	14	3547	9	0	9	0	23
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.13	5	11742	43	5	29	9	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
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

^top

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 MaxExpect - scored higher in this pairwise comparison

1. Total counts & total scores for MaxExpect

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

Performance of PknotsRG - scored lower in this pairwise comparison

1. Total counts & total scores for PknotsRG

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