Additional file 1.

The supplement includes the mathematical formulas for computing the probability of a motif site given a Markov model, the algorithmic pseudo-code for the DNJ method, and the description of the parameter estimation for our model. It also contains supplemental materials for the main results as well as other additional results, such as the application for protein domain identification, the comparison of computational time, and so on.

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Huang et al. BMC Bioinformatics 2006 7:279   doi:10.1186/1471-2105-7-279