IHF is a member of the histone-like proteins that bind to many sequence-specific but degenerate DNA sites, and affect processes that require DNA duplex destabilization such as DNA replication, recombination, and transcription. A positional weight matrix is derived from a set of known IHF binding sites using a physical description of possible dinucleotides. Based on the positional weight matrix, a hidden semi-Markov model is developed to simulate the IHF binding sites in E. coli DNA as well as for detecting putative binding sites in E. coli DNA. This is joint work with Simon Tavare' and Richard Deonier.