A fast structural multiple alignment method for long RNA sequences

Tabei, Yasuo; Kiryu, Hisanori; Kin, Taishin; Asai, Kiyoshi

doi:10.1186/1471-2105-9-33

BMC Bioinformatics

Table 2 Accuracies for the original multiple alignment dataset. SPS and MCC values (%) for the original multiple alignment dataset are presented. Each family has 5 RNA sequences. Family: Rfam family name. %id: average sequence identity. length: average sequence length (bases) in each family. Average(all): the average SPS or MCC for all families. Average(sub): the average SPS or MCC for the subset of families with an average sequence length of less than or equal to 100 bases. Because PMmulti and Stemloc were unable to align all data, the proportion of data that was aligned is given in parentheses as no. of sequences aligned/total no. of sequences. FoldalignM consists of two modes: FoldalgnM_FoldalignM and FoldalignM_McCaskill, which are separately evaluated and indicated as FoldalignM(1) and FoldalignM(2) respectively.

From: A fast structural multiple alignment method for long RNA sequences

SPS:Family	%id	length	MXSCARNA	Murlet	ProbCons	MAFFT	ClustalW	StrAl	RNASampler
IRE	62	29	98	96	93	89	77	83	92
s2m	78	43	96	96	96	96	96	96	95
UnaL2	78	54	95	98	98	96	92	94	82
Hammerhead_3	71	55	96	94	93	89	83	89	91
SECIS	42	64	65	66	65	52	45	56	46
sno_14q_I_II	71	74	90	95	96	93	93	87	71
tRNA	48	76	87	87	87	84	76	82	87
ctRNA_pGA1	74	80	88	86	85	88	84	86	89
Tymo_tRNA	70	83	84	83	82	75	75	79	77
Y	64	95	71	72	72	73	65	64	65
SRP_bact	52	95	71	71	70	66	70	62	66
Purine	55	100	74	77	77	78	75	81	69
5S_rRNA	60	117	88	89	89	86	86	86	83
S_box	66	130	79	80	78	78	68	72	67
U4	67	141	79	81	80	79	79	78	69
RFN	65	150	86	87	87	88	81	80	81
5_8S_rRNA	67	154	91	93	93	90	88	89	78
U1	60	158	81	81	79	79	79	76	74
Telomerase_cil	56	171	48	50	49	43	38	41	37
Lysine	50	180	78	81	79	72	70	76	72
U2	66	185	76	76	75	71	71	73	71
U17	75	214	91	93	93	89	89	87	81
U3	51	246	43	44	44	47	41	40	34
SRP_euk_arch	46	294	50	56	47	42	42	48	44
tmRNA	46	373	48	50	50	47	46	39	42
RnaseP_bact_b	64	387	82	80	79	78	74	74	66
Telomerase_vert	66	463	69	70	69	69	66	64	65
Average(all)			78	79	78	75	72	73	70
Average(sub)			85	85	85	82	78	80	78
SPS:Family	RNAlara	Locarna	FoldalignM(1)	FoldalignM(2)	MARNA	PMmulti	Stemloc
IRE	85	88 (100/100)	87 (99/101)	85 (97/100)	92	90 (101/101)	87 (101/101)
s2m	96	99 (43/50)	95 (50/50)	95 (47/50)	94	98 (44/50)	93 (50/50)
UnaL2	93	93 (78/89)	89 (75/89)	86 (87/89)	88	87 (75/89)	75 (89/89)
Hammerhead_3	88	80 (100/100)	79 (99/100)	77 (97/100)	89	87 (77/100)	94 (100/100)
SECIS	48	47 (62/63)	46 (63/63)	44 (63/63)	49	39 (63/63)	60 (60/63)
sno_14q_I_II	78	76 (98/98)	73 (98/98)	61 (97/98)	67	73 (97/98)	89 (97/98)
tRNA	91	82 (103/103)	90 (100/103)	78 (97/103)	59	86 (103/103)	88 (103/103)
ctRNA_pGA1	86	74 (20/28)	75 (28/28)	74 (27/28)	79	72 (20/28)	84 (28/28)
Tymo_tRNA	79	78 (49/59)	68 (59/59)	68 (56/59)	66	71 (49/59)	57 (57/59)
Y	56	49 (21/24)	50 (24/24)	47 (24/24)	60	43 (11/24)	68 (23/24)
SRP_bact	63	62 (70/70)	64 (70/70)	56 (67/70)	56	61 (63/70)	60 (67/70)
Purine	64	65 (45/45)	64 (45/45)	62 (45/45)	64	65 (45/45)	37 (45/45)
5S_rRNA	85
S_box	57
U4	71
RFN	78
5_8S_rRNA	81
U1	74
Telomerase_cil	32
Lysine	59
U2	71
U17	79
U3	32
SRP_euk_arch	42
tmRNA	34
RnaseP_bact_b	66
Telomerase_vert	51
Average(all)	68
Average(sub)	77	74	73	69	72	73	74
MCC:Family	%id	length	MXSCARNA	Murlet	ProbCons	MAFFT	ClustalW	StrAl	RNASampler
IRE	62	29	90	91	75	72	65	43	89
S2m	78	43	84	83	84	84	84	84	81
UnaL2	78	54	52	70	51	53	51	50	51
Hammerhead_3	71	55	99	95	93	86	72	79	96
SECIS	42	64	76	60	55	35	23	37	73
sno_14q_I_II	71	74	93	98	93	93	91	91	95
tRNA	48	76	91	89	86	84	76	83	95
ctRNA_pGA1	74	80	96	93	88	89	81	92	94
Tymo_tRNA	70	83	87	85	75	73	72	80	90
Y	64	95	95	85	86	83	67	83	94
SRP_bact	52	95	81	72	54	50	58	57	83
Purine	55	100	90	94	90	86	80	84	91
5S_rRNA	60	117	75	79	69	70	69	70	70
S_box	66	130	90	87	86	81	76	81	86
U4	67	141	75	71	62	62	54	65	67
RFN	65	150	84	83	84	84	82	83	82
5_8S_rRNA	67	154	58	51	47	45	41	46	52
U1	60	158	70	68	61	56	60	57	71
Telomerase	56	171	65	41	28	21	24	31	60
Lysine	50	180	87	90	76	66	63	71	89
U2	66	185	73	76	58	51	62	59	77
U17	75	214	79	80	78	76	75	72	72
U3	51	246	46	26	22	19	46	21	39
SRP_euk_arch	46	294	72	75	46	37	35	49	72
tmRNA	46	373	51	54	50	49	43	42	49
RNaseP_bact_b	64	387	73	58	63	58	53	60	37
Telomerase	66	463	64	51	47	44	40	36	53
Average(all)			78	74	67	63	61	63	74
Average(sub)			86	85	77	74	68	72	86
MCC:Family	RNAlara	Locarna	FoldalignM(1)	FoldalignM(2)	MARNA	PMmulti	Stemloc
IRE	81	89	85	89	82	89	81
s2m	84	83	85	86	79	85	84
UnaL2	53	53	53	51	51	50	45
Hammerhead_3	95	94	87	91	95	91	98
SECIS	63	74	74	75	57	67	78
sno_14q_I_II	92	87	92	84	81	93	85
tRNA	95	87	95	87	67	90	95
ctRNA_pGA1	97	95	96	96	95	94	95
Tymo_tRNA	85	75	87	82	62	82	83
Y	86	87	94	89	87	83	93
SRP_bact	65	87	86	83	63	80	69
Purine	77	89	88	88	82	86	89
5S_rRNA	72
S_box	72
U4	60
RFN	79
5_8S_rRNA	46
U1	60
Telomerase	39
Lysine	58
U2	63
U17	63
U3	21
SRP_euk_arch	42
tmRNA	40
RNaseP_bact_b	65
Telomerase	28
Average(all)	65
Average(sub)	81	83	85	83	75	83	83

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com