We have built a whole genome multiple alignment of the three currently available mammalian genomes using a fully automated pipeline which combines the local/global approach of the Berkeley Genome Pipeline and the LAGAN program. The strategy is based on progressive alignment, and consists of two main steps: (1) alignment of the mouse and rat genomes; and (2) alignment of human to either the mouse-rat alignments from step 1, or the remaining unaligned mouse and rat sequences. The resulting alignments demonstrate high sensitivity, with 87% of all human gene-coding areas aligned in both mouse and rat. The specificity is also high: <7% of the rat contigs are aligned to multiple places in human and 97% of all alignments with human sequence > 100kb agree with a three-way synteny map built independently using predicted exons in the three genomes. At the nucleotide level <1% of the rat nucleotides are mapped to multiple places in the human sequence in the alignment; and 96.5% of human nucleotides within all alignments agree with the synteny map. The alignments are publicly available online, with visualization through the novel Multi-VISTA browser that we also present.

In x-ray and gamma-ray spectroscopy, it is desirable to have detectors with high energy resolution and high absorption efficiency. At LLNL, we have developed superconducting tunnel junction-based single photon x-ray detectors with thin film absorbers that have achieved these goals for photon energies up to 1 keV. However, for energies above 1 keV, the absorption efficiency of these thin-film detectors decreases drastically. We are developing the use of high-purity superconducting bulk materials as microcalorimeter absorbers for high-energy x-rays and gamma rays. The increase in absorber temperature due to incident photons is sensed by a superconducting transition-edge sensor (TES) composed of a Mo/Cu multilayer thin film. Films of Mo and Cu are mutually insoluble and therefore very stable and can be annealed. The multilayer structure allows scaling in thickness to optimize heat capacity and normal state resistance. We measured an energy resolution of 70 eV for 60 keV incident gamma-rays with a 1 x 1 x 0.25 mm{sup 3} Sn absorber. We present x-ray and gamma-ray results from this detector design with a Sn absorber. We also propose the use of an active negative feedback voltage bias to improve the performance of our detector and show preliminary results.

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