The development of genome sequencing and DNA microarray analysis of gene expression gives rise to the demand for data-mining tools. BioProspector, a C program using a Gibbs sampling strategy, examines the upstream region of genes in the same gene expression pattern group and looks for regulatory sequence motifs. BioProspector uses zero to third-order Markov background models whose parameters are either given by the user or estimated from a specified sequence file. The significance of each motif found is judged based on a motif score distribution estimated by a Monte Carlo method. In addition, BioProspector modifies the motif model used in the earlier Gibbs samplers to allow for the modeling of gapped motifs and motifs with palindromic patterns. All these modifications greatly improve the performance of the program. Although testing and development are still in progress, the program has shown preliminary success in finding the binding motifs for Saccharomyces cerevisiae RAP1, Bacillus subtilis RNA polymerase, and Escherichia coli CRP. We are currently working on combining BioProspector with a clustering program to explore gene expression networks and regulatory mechanisms. For a copy of the program and documentation for UNIX systems, please contact xliu@smi.stanford.edu.
Chemical vapor deposition by Au-catalyzed decomposition of GeH 4 has been used to grow Ge nanowires on single-crystal silicon. The nanowires grow over the temperature range ∼320−380 °C under the conditions used, probably by the vapor−liquid−solid (VLS) process. The lowtemperature growth aids integration with conventional electronic devices. At the optimum temperature near 320 °C, many of the nanowires are epitaxially oriented with the substrate crystal structure, growing in 〈111〉 directionssat an oblique angle on (001)-oriented Si substrates and nearly vertically on Si(111). High-resolution transmission electron microscopy confirms that the nanowires grow in the 〈111〉 directions and that the crystal lattice continues from the substrate into the nanowires. Transmission electron microscopy also shows that the nanowires contain very few crystalline defects. Au-containing nanoparticles (possibly γ-phase Au 0.6 Ge 0.4 ) are found at the tips of the nanowires, but no Au can be detected within the nanowires themselves.
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