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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.

From: Multiple sequence alignment with user-defined anchor points

  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