Fig. 12.

The local E2pair model. In the local version of the E2pair model, unaligned regions can occur at the N or C-terminus or in between two homologous regions. The length of the unaligned regions is controlled by the Bernoulli parameter q (the expected length of a nonhomologous region is q/(1−q)), and the expected number of nonhomologous regions is r/(1−r). The residue frequencies f ¹ and f ² are background distribution for the nonhomologous regions. In between the BB and the EE states a homologous region between the two sequences occurs according to the E2pair global model in Fig. 11 b. The global alignment case corresponds to setting q=r=0