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Table 3 Comparing S2A2 matrix with other methods for sequence alignment accuracies on the ProSup benchmark

From: (PS)2-v2: template-based protein structure prediction server

Method Tce Tme Tie σ0e
S2A2a 8732 947 7198 53.4
S2A2 + PSSMa 9470 868 6998 58.7
SSALNb 9256 1115 7245 58.3
SPARKSc - - - 57.2
prof_sim 8009 4505 3142 43.6
PSI-BLAST 6733 4938 3452 36.4
FASTAd 5340 3003 7452 31.4
  1. aThis work.
  2. bResults from Qiu and Elber [10].
  3. cResults from Zhou and Zhou [9].
  4. dResults from Domingues et al. [15].
  5. eTc and Tm are total numbers of correctly aligned and missed residue pairs, respectively; Ti is the total number of incorrect aligned pairs; σ0 is the average percentage of correctly aligned residues