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We study a new data mining problem concerning the discovery of frequent agreement subtrees (FASTs) from a set of phylogenetic trees. A phylogenetic tree, or phylogeny, is an unordered tree in which the order among siblings is unimportant. Furthermore, each leaf in the tree has a label representing a taxon (species or organism) name, whereas internal nodes are unlabeled. The tree may have a root, representing...
In this paper we propose a new method for aligning two RNA secondary structures by taking into account the presence of conserved RNA substructures, or constraints, in the alignment process. Our method allows the incorporation of specific knowledge about the RNA structures being analyzed while computing their alignment and thus is very useful for RNA motif detection. We develop statistical measures...
Support vector machines (SVMs) are a state-of-the-art machine learning tool widely used in speech recognition, image processing and biological sequence analysis. An essential step in SVMs is to devise a kernel function to compute the similarity between two data points in Euclidean space. In this paper we present a new kernel that takes advantage of both global and local structural information in RNAs...
In this paper we present RADAR, a web-based toolkit for RNA data analysis and research. The toolkit is capable of performing database search, multiple structure alignment, and pairwise structure comparison. In addition, RADAR provides two salient features: (1) constrained alignment of RNA secondary structures, and (2) prediction of the consensus for a set of RNA secondary structures. RADAR assists...
Currently, phylogenetic tree techniques are being used in multiple areas, from tree of life problems to pathogen recognition to drug discovery. With all of these applications for phylogenetic tree techniques, methods are needed to exploit the knowledge modeled in phylogenetic trees more thoroughly. One such information point of interest is the behavior of frequent patterns in phylogenetic trees. While...
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