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Table 1 Performance of seven protein multi-alignment programs on the IRMBASE 1.0 database of benchmark alignments. Percentage values are sum-of-pairs scores, i.e. the percentage of correctly aligned residue pairs of ROSE motifs contained in the IRMBASE sequence families.

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

Method ref1 ref2 ref3 Total
DIALIGN-T 94.07% 92.69% 92.68% 93.14%
DIALIGN 2.2 92.26% 92.72% 91.87% 92.28%
T-COFFEE 1.37 91.18% 85.61% 87.81% 88.20%
PROBCONS 1.09 66.74% 68.30% 77.92% 70.98%
POA V2 90.26% 43.61% 36.85% 56.91%
MUSCLE 3.5 36.16% 37.84% 52.30% 42.10%
CLUSTAL W 1.83 8.02% 12.69% 20.16% 13.62%