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Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

Description: EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.
Date: December 10, 2007
Creator: Haas, B J; Salzberg, S L; Zhu, W; Pertea, M; Allen, J E; Orvis, J et al.
Partner: UNT Libraries Government Documents Department

Recent Physics Results from NSTX

Description: The National Spherical Torus Experiment (NSTX) has made considerable progress in advancing the scientific understanding of high performance long-pulse plasmas needed for ITER and future low-aspect-ratio Spherical Torus (ST) devices. Plasma durations up to 1.6s (5 current redistribution times) have been achieved at plasma currents of 0.7 MA with non-inductive current fractions above 65% while achieving {beta}{sub T} and {beta}{sub N} values of 16% and 5.7 (%mT/MA), respectively. Newly available Motional Stark Effect data has allowed systematic study and validation of current drive sources and improved the understanding of ''hybrid''-like scenarios. In MHD research, six mid-plane ex-vessel radial field coils have been utilized to infer and correct intrinsic error fields, provide rotation control, and actively stabilize the n=1 resistive wall mode at ITER-relevant low plasma rotation values. In transport and turbulence, the low aspect ratio and wide range of achievable {beta} in NSTX provide unique data for confinement scaling studies. A new high-k scattering diagnostic is investigating turbulent density fluctuations with wavenumbers extending from ion to electron gyro-scales. In the area of energetic particle research, cyclic neutron rate drops have been associated with the destabilization of multiple large Toroidal Alfven Eigenmodes (TAEs) similar to the ''sea-of-TAE'' modes predicted for ITER. Three wave coupling processes between energetic particle modes and TAEs have also been observed for the first time. In boundary physics, advanced shape control has been utilized to study the role of magnetic balance in H-mode access and ELM stability. Peak divertor heat flux has been reduced by a factor of 5 using an H-mode compatible radiative divertor, and Lithium conditioning has demonstrated particle pumping and improved thermal confinement. Finally, non-solenoidal plasma start-up research is particularly important for the ST, and Coaxial Helicity Injection has now produced 160kA plasma currents on closed magnetic flux surfaces.
Date: October 5, 2006
Creator: Menard, J E; Bell, M G; Bell, R E; Bialek, J M; Boedo, J A; Bush, C E et al.
Partner: UNT Libraries Government Documents Department