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A major challenge in bioinformatics is discovering functional regions in biosequences. These regions may correspond to folded structures, physicochemical functionality, or mutation hotspots. The identification of functional regions in biosequences is essential to better understand biological mechanisms, design new drugs, and uncover novel knowledge concerning sporadic and genetic diseases. Pattern analysis and WeMine aligned pattern clustering (APC) systems enable the discovery of conserved regions with adaptive width and mutations, including frameshift, without relying on prior knowledge or exhaustive search. They align and rank patterns in local and distant correlated regions with statistical support within, and between, sequences. This chapter provides an overview of the WeMine APC and its utility in identifying functional regions such as protein binding sites, predicting pairwise interactions between protein-DNA and protein-protein network, and finding correlations among patterns and residues with class labels. Pattern analysis and WeMine APC could play an important role in personalized medicine, gene therapy, biomarker identification and drug discovery.
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