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Table 2 Performance of seven protein multi-alignment programs on IRMBASE using column scores as quality criterion. Thus, percentage values denote the percentage of correct alignment columns of the ROSE motifs in IRMBASE

From: DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment

Method

ref1

ref2

ref3

Total

DIALIGN-T

82.28%

78.36%

79.71%

80.12%

DIALIGN 2.2

79.46%

77.82%

78.24%

78.51%

T-COFFEE 1.37

75.35%

66.60%

69.21%

70.19%

PROBCONS 1.09

33.13%

37.95%

51.26%

40.78%

POA V2

73.00%

12.46%

07.45%

30.97%

MUSCLE 3.5

09.41%

10.89%

22.37%

14.22%

CLUSTAL W 1.83

00.00%

00.83%

05.14%

01.92%