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Table 1 Evaluation of alignment methods on the SABmark benchmark

From: SFESA: a web server for pairwise alignment refinement by secondary structure shifts

Methods SABmark_TWI (209) SABmark_SUP (425)
PROMALS 46.2 71.10
SFESA (O) + PROMALS 47.3 71.30
SFESA (O + G) + PROMALS 48.0 71.80
SFESA (O + G + M) + PROMALS 47.9 71.90
SFESA (O + G + M + S) + PROMALS 48.1 72.10
HHpred 40.7 68.9
SFESA (O) + HHpred 40.6 69.0
SFESA (O + G) + HHpred 41.3 69.1
SFESA (O + G + M) + HHpred 41.4 69.6
SFESA (O + G + M + S) + HHpred 41.3 69.4
CNFpred 41.5 66.1
SFESA (O) + CNFpred 41.6 66.4
SFESA (O + G) + CNFpred 42.3 67.0
SFESA (O + G + M) + CNFpred 42.4 67.4
SFESA (O + G + M + S) + CNFpred 42.2 66.9
  1. Average Q-scores of two SABmark [25] data sets (‘TWI’ for ‘Twilight Zone’ set, ‘SUP’ for ‘Superfamilies’ set) are shown. The Q-score is the number of correctly aligned residue pairs in the test alignment divided by the total number of aligned residue pairs in the reference alignment. One pair of domains is selected randomly from each group in the SABmark sets. For each set, the number in the parentheses is the number of alignments tested. Bold numbers indicate the best performance in the subsection