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This paper is concerned wth the physical mapping of DNA molecules using data about the hybridization of oligonucleotide probes to a library of clones. In mathematical terms, the DNA molecule corresponds to an interval on the real line, each clone to a subinterval, and each probe occurs at a finite set of points within the interval. A stochastic model for(More)
The goal of physical mapping of the genome is to reconstruct a strand of DNA given a collection of overlapping fragments, or clones, from the strand. We present several algorithms to infer how the clones overlap, given data about each clone. We focus on data used to map human chromosomes 21 and Y, in which relatively short substrings, or probes, are(More)
A current barrier for successful rational drug design is the lack of understanding of the structure space provided by the proteins in a cell that is determined by their sequence space. The protein sequences capable of folding to functional three-dimensional shapes of the proteins are clearly different for different organisms, since sequences obtained from(More)
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Here, we studied systematically the association between amino acids, the constituents of protein sequences in datasets of different hierarchy, i.e. genome (human), protein type (membrane proteins), protein family (specific types of membrane receptors and transporters) and transmembrane helices versus loops (either for membrane proteins in general or(More)
Protein sequence data is abundant, yet derivation of structural features from sequence alone is generally restricted to prediction of domain architecture, secondary structure elements and motifs. Precise feature boundaries cannot be determined reliably, and it is unknown to what extent these features constitute fundamental building blocks of protein(More)
The Cray XT is an MPP system that scales up to 32K nodes using a bidirectional 3-dimensional torus intercon-nection network. Four virtual channels are used to provide point-to-point flow control and deadlock avoidance. Using virtual channels avoids unnecessary head-of-line (HoL) blocking for different network traffic flows, however, the extent to which(More)