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By Althaus E.

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Each entry in the table is the score computed by the evaluation program provided with the BAliBase library. In brackets we give the percentage relative to the best program for this example. In addition, we provide an average for each group. The results show that our approach was on average superior to all other programs. Our comparison with other programs reveals that computing near-optimal alignments does pay off in terms of quality, because our approach produced on average the biologically most meaningful alignments.

Althaus et al. Table 3. 8; 1 13 3:14. 9; 1 5 2. 9; 19 65 7:08. 9; 1 11 5:15. 3; 1 6 2. 6; 1 14 17. 0; 1 10 34. 8; 1 6 4. 7; 1 17 30. 0; 1 10 20. 9; 1 7 16. 4; 1 12 7:51. 5; 1 18 29:42. 0; 10 50 7:49. 6; 1 14 9:24. 1; 1 27 40:38. 0; 1 14 2:08. 0]; 1 51 10:02:04. 4; 1 16 6:55. 7]; 1 45 12:33:06. 3]; 1 34 10:08:14. 1]; 1 120 10:23:22. 4]; 9 149 10:06:15. 8]; 1 109 10:28:33. 0]; 1 92 10:30:51. 0]; 1 30 10:37:44. 3]; 1 31 10:00:06. 3. Comparison with other programs We compared our algorithm with the most recent structural alignments algorithms, considering the overall best performing programs from the survey [27]: PRRP, ClustalX, and Dialign, together with a recently published program T-Coffee [22], which generally outperforms the other programs.

Comparison with other programs We compared our algorithm with the most recent structural alignments algorithms, considering the overall best performing programs from the survey [27]: PRRP, ClustalX, and Dialign, together with a recently published program T-Coffee [22], which generally outperforms the other programs. The source code of all these programs was downloaded and they were run with default parameters. We disregarded all other programs, since they perform significantly worse (see [27]).

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