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Table 3 Accuracies for the BRAlibaseII multiple alignment dataset. SPS and MCC values (%) for the BRAlibaseII 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 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

MXSCARNA

Murlet

ProbCons

MAFFT

ClustalW

StrAl

RNASampler

 

tRNA

69

76

91

91

91

89

85

89

92

 

Intron_gpII

64

80

79

80

80

77

75

79

74

 

5S_rRNA

70

117

89

90

90

89

88

89

90

 

U5

72

118

74

75

76

72

72

73

78

 

SRP

67

300

88

88

88

87

87

86

82

 

Average(all)

  

84

85

85

83

81

83

83

 

Average(sub)

  

83

84

84

82

80

82

83

 

SPS:Family

RNAlara

Locarna

FoldalignM(1)

FoldalignM(2)

MARNA

PMmulti

Stemloc

   

tRNA

95

93 (98/98)

94 (97/98)

90 (91/98)

79 (98/98)

90 (89/98)

88 (98/98)

   

Intron_gpII

75

71 (89/92)

70 (92/92)

67 (89/92)

76 (92/92)

77 (61/92)

77 (92/92)

   

5S_rRNA

93

92 (89/89)

92 (88/89)

89 (89/89)

58 (78/89)

85 (89/89)

72 (89/89)

   

U5

80

77 (109/109)

72 (108/109)

69 (107/109)

85 (74/109)

56 (105/109)

64 (109/109)

   

SRP

82

83 (84/93)

        

Average(all)

85

83

        

Average(sub)

86

83

82

79

74

77

75

   

MCC:Family

%id

length

MXSCARNA

Murlet

ProbCons

MAFFT

ClustalW

StrAl

RNASampler

RNAlara

tRNA

69

76

94

92

91

90

83

88

94

93

Intron_gpII

64

80

82

80

77

76

74

74

80

79

5S_rRNA

70

117

71

69

67

68

67

69

69

70

U5

72

118

80

75

70

66

66

69

77

72

SRP

67

300

75

72

68

67

68

65

71

63

Average(all)

  

80

78

75

73

72

73

78

76

Average(sub)

  

82

79

76

75

72

75

80

79

MCC:Family

Locarna

FoldalignM(1)

FoldalignM(2)

MARNA

PMmulti

Stemloc

    

tRNA

92

96

92

80

93

93

    

Intron_gpII

80

76

80

78

76

76

    

5S_rRNA

71

72

71

59

70

68

    

U5

74

70

69

60

61

78

    

SRP

73

         

Average(all)

78

         

Average(sub)

79

79

78

69

75

79

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