Table 3  DIALIGN alignment scores for anchored and non-anchored alignment of five reference test sets from BAliBASE. As anchor points, we used the so-called core-blocks in BAliBASE, thereby enforcing biologically correct alignments of the input sequences. The figures in the first and second line refer to the sum of DIALIGN alignment scores of all protein families in the respective reference set. Line four contains the number of sequence sets where the anchoring improved the alignment score together with the total number of sequence sets in this reference set. Our test runs show that on these test data, biologically meaningful alignments do not have higher DIALIGN scores than alignments produced by the default version of our program.
Alignment scores
Ref1  Ref2  Ref3  Ref4  Ref5  Total
non-anchored  53,613  269,009  283,273  36,515  29,214  671,624
anchored  53,417  265,966  283,136  36,611  29,257  668,387
ratio  0.996  0.988  0.999  1.002  1.001  0.995
score improved  23/82  13/23  4/23  6/16  4/12  50/156