RHOM (Research of HOMogeneous regions in DNA sequences) is software designed for the use of hidden Markov chain models for the segmentation of DNA sequences in homogeneous regions. R’HOM makes it possible to estimate a more realistic model of DNA sequence composition than a homogeneous Markov chain model and then to segment the sequence under this model. It has been used in particular to look for horizontal transfers in B. subtilis and to estimate models designed to calculate the significance of word counting. R’HOM has been developed in cooperation with the Laboratoire Statistique et Génome in Evry.
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