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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)
We study model checking for a first-order linear-time temporal logic. We present the computation model: abstract description of state machines (ASMs), in which data and data operations are described using abstract sort and uninterpreted function symbols. ASMs are suitable for describing Register Transfer level designs. We define a first-order linear-time(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)
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)
Large sets of bioinformatical data provide a challenge in time consumption while solving the cluster identification problem, and that is why a parallel algorithm is so needed for identifying dense clusters in a noisy background. Our algorithm works on a graph representation of the data set to be analyzed. It identifies clusters through the identification of(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)
Detection of RNA polymerase II promoters and polyadenylation sites helps to locate gene boundaries and can enhance accurate gene recognition and modeling in genomic DNA sequence. We describe a system which can be used to detect polyadenylation sites and thus delineate the 3' boundary of a gene, and discuss improvements to a system first described in Matis(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)