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Table 1 Evaluation of MSARC variants

From: MSARC: Multiple sequence alignment by residue clustering

MSARC variant

 

SP/TC scores

Alt. indels

Weighted

Multilevel

 

All

RV11

RV12

RV20

RV30

RV40

RV50

yes

yes

no

 

87 . 6 57 . 1

69 . 9 46.3

94 . 5 85.7

92 . 5 39.2

83 . 7 47.2

93 . 2 62.3

88.7 51.6

yes

yes

yes

 

87 . 6 57.0

69.7 46 . 5

94 . 5 85 . 8

92 . 5 39.0

83.6 46.9

93 . 2 61.8

88.7 51 . 9

yes

no

no

 

87.5 56.6

69.3 45.5

94.4 85.6

92 . 5 39.6

83 . 7 47 . 6

93.0 61.2

88.6 49.6

yes

no

yes

 

87.5 56.6

69.6 45.6

94 . 5 85 . 8

92 . 5 39.3

83.4 47.0

93.1 61.4

88.4 49.6

no

yes

no

 

87.5 57.0

69.2 45.6

94.4 85.7

92 . 5 39.5

83.5 47.1

93 . 2 62.2

89 . 0 51 . 9

no

yes

yes

 

87.5 57 . 1

69.2 46.2

94.4 85.6

92 . 5 39.2

83 . 7 47.7

93 . 2 62 . 4

88.7 51.6

no

no

no

 

87.5 56.6

69.4 45.6

94 . 5 85.7

92 . 5 39 . 7

83.5 46.9

93.0 61.3

88.5 49.7

no

no

yes

 

87.5 56.7

69.5 45.7

94.4 85.7

92 . 5 39.1

83.5 47.0

93.1 61.7

88.6 49.7

  1. All the combinations of the following options are evaluated: (dis-)allowing for neighboring insertions and deletions in pairwise alignments, (not) weighting sequence pairs in consistency transformation and (not) using multilevel scheme in residue clustering. Entries show the mean SP and TC scores for each alignment algorithm on the whole BAliBASE 3.0 dataset and each of its series. All scores are multiplied by 100. Best results in each column are shown in bold.