DNA Sequence alignment Vlll Still figuring out how to choose the mismatch penalty m Target frequencies: qi=p,p e/ij =In(q;/p:p )/A If you want to find regions with R% identities r=R/100q=r4q=(1n)12() Set s=1 Then m=Si=S/Si=In(q /p pi ))/(In(qi/pip1)/ (]) →m=n4(1)/3)n(4DNA Sequence Alignment VIII Still figuring out how to choose the mismatch penalty m Target frequencies: qij = pi pj e λ sij sij = l n ( qij / pi pj ⇒ )/ If you want to find regions with R% identities: r = R /100 qii = r/4 qij = (1-r)/12 (i,j) Set sii = 1 Then m = sij = sij/sii = ln(qij / pi pj )/ λ) / (ln(qii / pi pi )/ λ (i ≠j) ⇒ m = ln(4(1-r)/3)/ln(4r) λ