Reseracher propose an algorithm that integrates two important aspects of a motif’s significance — overrepresentation and cross-species conservation — into one probabilistic score. The algorithm allows the input orthologous sequences to be related by any user-specified phylogenetic tree. It is based on the Expectation-Maximization technique, and scales well with the number of species and the length of input sequences.
They evaluate the algorithm on synthetic data, and also present results for data sets from yeast, fly, and human.
Source : BMC Bioinformatics