Improving Gene-finding in Chlamydomonas reinhardtii:GreenGenie2

<p>Abstract</p> <p>Background</p> <p>The availability of whole-genome sequences allows for the identification of the entire set of protein coding genes as well as their regulatory regions. This can be accomplished using multiple complementary methods that include ESTs, homology searches and <it>ab initio </it>gene predictions. Previously, the Genie gene-finding algorithm was trained on a small set of <it>Chlamydomonas </it>genes and shown to improve the accuracy of gene prediction in this species compared to other available programs. To improve <it>ab initio </it>gene finding in <it>Chlamydomonas</it>, we assemble a new training set consisting of over 2,300 cDNAs by assembling over 167,000 <it>Chlamydomonas </it>EST entries in GenBank using the EST assembly tool PASA.</p> <p>Results</p> <p>The prediction accuracy of our cDNA-trained gene-finder, GreenGenie2, attains 83% sensitivity and 83% specificity for exons on short-sequence predictions. We predict about 12,000 genes in the version <it>v3 Chlamydomonas </it>genome assembly, most of which (78%) are either identical to or significantly overlap the published catalog of <it>Chlamydomonas </it>genes <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>. 22% of the published catalog is absent from the GreenGenie2 predictions; there is also a fraction (23%) of GreenGenie2 predictions that are absent from the published gene catalog. Randomly chosen gene models were tested by RT-PCR and most support the GreenGenie2 predictions.</p> <p>Conclusion</p> <p>These data suggest that training with EST assemblies is highly effective and that GreenGenie2 is a valuable, complementary tool for predicting genes in <it>Chlamydomonas reinhardtii</it>.</p

Search for Intrinsic Excitations in 152Sm

The 685 keV excitation energy of the first excited 0+ state in 152Sm makes it an attractive candidate to explore expected two-phonon excitations at low energy. Multiple-step Coulomb excitation and inelastic neutron scattering studies of 152Sm are used to probe the E2 collectivity of excited 0+ states in this "soft" nucleus and the results are compared with model predictions. No candidates for two-phonon K=0+ quadrupole vibrational states are found. A 2+, K=2 state with strong E2 decay to the first excited K=0+ band and a probable 3+ band member are established.Comment: 4 pages, 6 figures, accepted for publication as a Rapid Communication in Physical Review

High precision branching ratio measurement for the superallowed β decay of [Formula Presented] A prerequisite for exacting tests of the standard model

Nonanalog Fermi and Gamow-Teller branches in the superallowed β decay of [Formula Presented] have been investigated using γ-ray and conversion-electron spectroscopy. Nine observed transitions, in conjunction with a recent shell model calculation, determine the branching ratio of the analog transition to be 99.5(1)%. The experimental upper limits for the Fermi decay to the [Formula Presented] and [Formula Presented] levels are in agreement with recent theoretical predictions. The [Formula Presented] value for the [Formula Presented] β decay is predicted to be 10405(9) keV. © 2003 The American Physical Society

Applied Plasma Research

Contains research objectives, summary of research and reports on four research projects.National Science Foundation (Grant GK-28282X1)National Science Foundation (Grant GK-33843

Gamma-ray spectroscopy at TRIUMF-ISAC: The new frontier of radioactive ion beam research

High-resolution gamma-ray spectroscopy is essential to fully exploit the unique scientific opportunities at the next generation radioactive ion beam facilities such as the TRTUMF Isotope Separator and Accelerator (TSAC). At IS AC the 871 spectrometer and its associated auxiliary detectors is optimize for p-decay studies while TIGRESS an array of segmented clover HPGe detectors has been designed for studies with accelerated beams. This paper gives a brief overview of these facilities and also presents recent examples of the diverse experimental program carried out at the STI spectrometer. © 2009 American Institute of Physics

Pennsylvania Folklife Vol. 30, No. 1

• The Allentown Academy: America\u27s First German Medical School • Amish Attitudes and Treatment of Illness • Germanic European Origins and Geographical History of the Southeastern Pennsylvania Dunkards • The Voyage of Bishop Naas 1733 • Segregation in Life, Segregation in Death: Landscape of an Ethnic Cemetery • Rest in Peace, Joseph Hewes! • Aldes un Neies / Old & Newhttps://digitalcommons.ursinus.edu/pafolklifemag/1089/thumbnail.jp