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Computational methods for gene identification in genomic sequences typically have two phases: coding region recognition and gene parsing. While there are a number of effective methods for recognizing coding regions (exons), parsing the recognized exons into proper gene structures, to a large extent, remains an unsolved problem. We have developed a computer(More)
This paper presents a computationally efficient algorithm, the Gene Assembly Program III (GAP III), for constructing gene models from a set of accurately-predicted 'exons'. The input to the algorithm is a set of clusters of exon candidates, generated by a new version of the GRAIL coding region recognition system. The exon candidates of a cluster differ in(More)
Matching two geometric objects in two-dimensional (2D) and three-dimensional (3D) spaces is a central problem in computer vision, pattern recognition, and protein structure prediction. In particular, the problem of aligning two polygonal chains under translation and rotation to minimize their distance has been studied using various distance measures. It is(More)
This paper focuses on "router-based" defense mechanisms, and whether they can provide effective solutions to network Denial-of-Service (DoS) attacks. Router-based defenses operate either on traffic aggregates or on individual flows, and have been shown, either alone or in combination with other schemes, e.g., traceback, to be reasonably effective against(More)
This paper presents a novel linear programming approach to do protein 3-dimensional (3D) structure prediction via threading. Based on the contact map graph of the protein 3D structure template, the protein threading problem is formulated as a large scale integer programming (IP) problem. The IP formulation is then relaxed to a linear programming (LP)(More)
MOTIVATION DNA microarray is a powerful high-throughput tool for studying gene function and regulatory networks. Due to the problem of potential cross hybridization, using full-length genes for microarray construction is not appropriate in some situations. A bioinformatic tool, PRIMEGENS, has recently been developed for the automatic design of PCR primers(More)
MOTIVATION Automatic decomposition of a multi-domain protein into individual domains represents a highly interesting and unsolved problem. As the number of protein structures in PDB is growing at an exponential rate, there is clearly a need for more reliable and efficient methods for protein domain decomposition simply to keep the domain databases(More)
UNLABELLED Palmitoylation is an important post-translational lipid modification of proteins. Unlike prenylation and myristoylation, palmitoylation is a reversible covalent modification, allowing for dynamic regulation of multiple complex cellular systems. However, in vivo or in vitro identification of palmitoylation sites is usually time-consuming and(More)