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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