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Table 7 Performance comparison of PROSITE patterns, Profile HMMs and SCFGs

From: A stochastic context free grammar based framework for analysis of protein sequences

  Size Method Max F1 Pr Rc Rc| Pr = 1.0
PS00219 12 PROSITE 0.94 1.00 0.89 0.89
  12 SCFG 1.00 1.00 1.00 1.00
PS00063 16 PROSITE 0.81 1.00 0.81 0.81
  16 Profile HMM 0.95 1.00 0.91 0.91
  16 SCFG 0.71 0.79 0.65 0.29
PS00307 7 PROSITE 0.52 0.36 0.94 0.94
  25 Profile HMM 1.00 1.00 1.00 1.00
  25 SCFG 0.91 1.00 0.84 0.84
MPI phosphatase - PROSITE No PROSITE pattern
  25 Profile HMM 0.96 1.00 0.92 0.92
  25 SCFG 0.94 0.98 0.89 0.85
Zinc finger 10-26 PROSITE Out of scope
  26 Profile HMM 0.79 0.76 0.82 0.21
  26 SCFG 0.81 0.75 0.87 0.21