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Table 4 Accuracies for Kiryu et al.'s dataset. SPS and MCC values (%) for Kiryu et al.'s dataset are presented. Each family has 10 RNA sequences. Family: Rfam family name. %id: average sequence identity. length: average sequence length (bases) in each family. Average(all): the results of the average value of the 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(nt) MXSCARNA Murlet ProbCons MAFFT ClustalW StrAl RNAlara
UnaL2 73 54 92 95 95 91 84 86 87
SECIS 41 64 70 73 68 44 35 59 53
tRNA 45 73 87 90 87 76 62 75 91
sno_14q_I_II 64 75 82 92 92 91 80 75 72
SRP_bact 47 93 58 61 61 60 61 48 56
THI 55 105 77 83 82 78 58 65 65
S_box 66 107 86 88 88 82 82 77 77
5S_rRNA 57 116 84 85 85 81 82 79 83
Retroviral_psi 92 117 97 97 97 97 96 97 97
RFN 66 140 89 91 90 91 83 80 86
5_8S_rRNA 61 154 85 88 87 84 78 81 75
U1 59 157 74 77 75 73 71 66 66
Lysine 49 181 75 77 75 66 60 68 59
U2 62 182 71 74 73 68 65 67 69
T-box 45 244 44 50 50 43 34 32 15
IRES_HCV 94 261 96 96 96 96 96 83 96
SRP_euk_arch 40 291 42 42 40 36 34 40 39
Average(all)    77 80 79 74 68 69 70
Average(sub)    82 86 85 80 73 75 77
SPS:Family RNASampler Locarna FoldalignM(1) FoldalignM(2) MARNA PMmulti Stemloc   
UnaL2 72 88 68 60 83 (5/5) 69 (5/5) 82 (5/5)   
SECIS 54 49 42 41 47 (5/5) 35 (5/5) 82 (5/5)   
tRNA 82 79 84 66 54 (5/5) 69 (5/5) 91 (5/5)   
sno_14q_I_II 64 57 45 34 49 (5/5) 39 (3/5) 77 (5/5)   
SRP_bact 54 52 55 51 43 (5/5) 36 (4/5) 47 (3/5)   
THI 68 65 65 62 62 (4/5) 58 (5/5) 71 (5/5)   
S_box 76 63 57 57 78 (5/5) 44 (5/5) 84 (5/5)   
5S_rRNA 77 79 74 70 71 (5/5) 57 (5/5) 77 (3/5)   
Retroviral_psi 96 95 91 91 96 (5/5) 87 (5/5) 75 (5/5)   
RFN 82 72 73 63 77 (5/5) 58 (4/5) 80 (5/5)   
5_8S_rRNA 69 75 56 31 64 (5/5) 58 (5/5) 73 (1/5)   
U1 63 68    50 (5/5)     
Lysine 71 55    58 (5/5)     
U2 65 64    65 (1/5)     
T-box 32 15    22 (5/5)     
IRES_HCV 93 75    92 (3/5)     
SRP_euk_arch 33 40    37 (5/5)     
Average(all) 68 64    62     
Average(sub) 72 70 64 57 52 60 76   
MCC:Family %id length(nt) MXSCARNA Murlet ProbCons MAFFT ClustalW StrAl RNAlara
UnaL2 73 54 42 41 46 36 24 32 44
SECIS 41 64 78 78 59 20 23 45 70
tRNA 45 73 93 97 91 85 65 85 97
sno_14q_I_II 64 75 87 91 91 91 66 75 87
SRP_bact 47 93 66 56 46 49 54 52 69
THI 55 105 71 70 70 62 38 48 58
S_box 66 107 90 89 87 79 77 75 76
5S_rRNA 57 116 75 67 62 64 53 66 69
Retroviral_psi 92 117 86 86 86 84 86 86 86
RFN 66 140 67 71 72 73 71 60 70
5_8S_rRNA 61 154 38 43 35 16 14 26 33
U1 59 157 69 61 57 56 61 52 56
Lysine 49 181 83 81 71 33 52 61 64
U2 62 182 74 71 56 38 39 58 68
T-box 45 244 72 78 80 51 41 26 0
IRES_HCV 94 261 63 62 62 63 26 34 63
SRP_euk_arch 40 291 70 63 40 21 23 38 33
Average(all)    72 71 65 54 48 54 61
Average(sub)    72 72 68 60 52 59 69
MCC:Family RNASampler Locarna FoldalignM(1) FoldalignM(2) MARNA PMmulti Stemloc   
UnaL2 51 42 57 50 36 18 39   
SECIS 78 80 75 80 40 64 77   
tRNA 94 96 95 89 51 91 98   
sno_14q_I_II 84 95 95 86 79 77 87   
SRP_bact 73 74 80 75 47 44 64   
THI 72 60 50 51 59 41 77   
S_box 86 82 83 87 83 55 88   
5S_rRNA 62 75 72 73 59 58 66   
Retroviral_psi 86 88 76 89 84 73 87   
RFN 69 69 67 70 65 58 72   
5_8S_rRNA 38 40 43 41 21 14 34   
U1 64 73    45     
Lysine 86 80    66     
U2 79 65    66     
T-box 44 1    2     
IRES_HCV 63 47    61     
SRP_euk_arch 62 64    52     
Average(all) 70 66    54     
Average(sub) 72 73 72 72 60 54 72