Klpek's Note Library

sequences alignment tools

BLAST

sequence-sequence alignment

PSI-BLAST

profile-sequence alignment

HMMER

HMM-sequence alignment

PROF_SIM and COMPASS

profile-profile alignment

HHSearch

HHSearch2

Alignment Quality Evaluation

plain MaxSub score

$$S_{Dev}=N_{correct}/min(L_q,L_p)$$

Modeler’s score

$$S_{Mod}=N_{correct}/L_{ali}$$

Balanced Score

$$S_{balanced}=(S_{Dev}+S_{Mod})$$