Figure 4
From: Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes
Prediction strategy. A. Example of the iterated HMM in Proteobacteria. The first seed profile hidden Markov model is created from the seed dif sequence of Escherichia coli, by searching for dif sequences in 28 genomes belonging to the genus Escherichia by means of fuzzy matching. Based on this initial profile hidden Markov model, dif sequences were predicted in the genomes of the closest genus to the Escherichia genus (in this case, Shigella) according to XerCD amino acid sequences. Subsequently, a new profile is created using the previous profile and the newly predicted dif sequences, and this new profile is used to predict in the second closest genus (in this case, Salmonella). In this way, profile creation and dif sequence prediction were repeated recursively in decreasing order of similarity of XerCD from the Escherichia sequence. In this way, iterated HMM is conducted for each phylum. B. Flow chart of the overall strategy.