SOAPindel: Efficient identification of indels from short paired reads Shengting Li, Ruiqiang Li, Heng Li, Jianliang Lu, Yingrui Li, Lars Bolund, Mikkel Schierup, and Jun Wang Genome Res. published 12 September 2012; doi:10.1101/gr.132480.111 http://genome.cshlp.org/content/early/2012/09/12/gr.132480.111.abstract.html We present a new approach to indel calling which explicitly exploits that indel differences between a reference and a sequenced sample make the mapping of reads less efficient. We assign all unmapped reads with a mapped partner to their expected genomic positions and then perform extensive de novo assembly on the regions with many unmapped reads to resolve homozygous, heterozygous and complex indels by exhaustive traversal of the de Bruijn graph. The method is implemented in the software SOAPindel and provides a list of candidate indels with quality scores. We compare SOAPindel to Dindel, Pindel and GATK on simulated data and find similar or better performance for short indels (10 bp) and higher sensitivity and specificity for long indels. A validation experiment suggests that SOAPindel has a false positive rate around 10% for long indels (5 bp) while still providing many more candidate indels than other approaches.
From http://www.isas.illinois.edu/atam/research/pima/whatispima.html PIMA (Portable Infrared Mineral Analyzer)* The PIMA is a shoebox-sized, portable infrared spectrometer that can be used for qualitative identification of the minerals in stone and low-fired clay artifacts. The instrument can be operated in the field or in a museum setting, and the analysis is totally non-destructive. PIMA requires no sample preparation and leaves no radiation damage. The PIMA window is held up against the flat surface of an artifact and the reading takes only 30-60 seconds, allowing the rapid collection of a large number of analyses. Measurements can be made on whole or partial artifacts, potsherds, rock chips, powders, and soil samples. PIMA spectroscopy uses the short wavelength infrared (SWIR) part of the electromagnetic spectrum (from 1300-2500 nanometers) and measures the reflected radiation from the surface of a sample. This measurement reveals the interatomic bond energies characteristic of specific minerals. The PIMA has been used successfully by geologists in the U.S., South America, Australia, and Europe for mineral exploration, studying the degree of crystallinity of minerals, and mapping alteration systems. Its immediate application to archaeology is in sourcing of stone and clay artifacts, providing another analytical tool to supplement and complement more costly and destructive techniques such as X-ray diffraction (XRD). PIMA analysis works best on minerals that contain hydroxyls (OH groups) such as phyllosilicates (including clay, chlorite and serpentine minerals), hydroxylated silicates (such as epidotes and amphiboles), sulphates (alunite, jarosite and gypsum) and carbonates. Dehydrated materials such as high-fired ceramics do not produce useable spectra (low-fired ceramics may work, but this has yet to be determined). The PIMA technology is expected to be most useful in providing mineral composition for museum artifacts that cannot be destructively sampled and in identifying potential sources of clay and stone in the field that can then be sampled for additional laboratory testing. * We are currently using a PIMA SP, purchased from Integrated Spectronics Pty Ltd, Australia . !-- For more information, see the PIMA SP web page/a. -- Spectra courtesy of Integrated Spectronics Pty Ltd. This material is based upon work supported by the National Science Foundation under Grant nos. 9971179 and 0203010. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation Contact Information ATAM Progam, ISAS Neil St. Lab University of Illinois at Urbana-Champaign (MC 568) 704 S. Neil St. Champaign, IL 61820 tel: 217-355-0757 email: wisarc illinois.edu
For a long time, I had long hair, because it's easier (and cheaper) to maintain. Then, in summer 2010 I was forced to get a fashionable short haircut in Qingdao. I was glad to have short hair in hot summer in China, which also made washing easier. But, the cost to maintain it is high (if you go to a decent hair salon in Kahala). Yesterday, a friend reminded me what we looked when we were younger, seven years younger, by sending me a picture taken at the Pali Lookout in 2005. OMG, I for the first time wish I had long hair.
What kind of committee would make such a demand for super short abstracts? I had an abstract of 800 words. (Yes, I know it is too long.) So, I just spent 30 mins to shorten it to less than 160 words. Here it is. ON THE EASTWARD SHIFT OF THE ARABIAN SEA OXYGEN MINIMUM ZONE Observations indicate that the upper part of the Arabian Sea oxygen minimum zone (ASOMZ; above 400 m) appears to the east of most productive regions along the western boundary of the Arabian Sea. There is no consensus about what causes the so-called “eastward shift.” We use a coupled biological/physical model to investigate the processes that determine the “eastward shift.” The physical component of the model is a variable-density, 6 1/2-layer model, with each layer corresponding to a distinct dynamic regime or water-mass type. Its biological component consists of a set of advective-diffusive equations in each layer that determine nitrogen concentration in five compartments, namely, nutrients, phytoplankton, zooplankton, and two size classes of detritus. In addition, the model contains an oxygen compartment that reacts to production and consumption of dissolved inorganic nitrogen in the biological system. We will show the relative roles of physical versus biological processes in generating the so-called “eastward shift” in the upper ASOMZ.
the following websites for short message service are recommended by my friends in America. I collected a lot of data from them. http://www.webopedia.com/quick_ref/textmessageabbreviations.asp http://www.comp.nus.edu.sg/~rpnlpir/ http://www.txtmania.com/messages/text.php http://www.chinadaily.com.cn/language_tips/auvideo/2009-08/27/content_8624761.htm http://www.lingo2word.com/index.php http://en.wikipedia.org/wiki/Text_messaging http://www.txt2nite.com/
仅限学术研究使用，严禁商业用途，作者和出版社如有异议，我立即删除附件。如果觉得本书比较好，请购买正版图书。也欢迎各位博友讨论本书内容。欢迎学术交流。 N. L. CAROTHERS Bowling Green State University Preface These are notes for a graduate topics course offered on several occasions to a rather diverse group of doctoral students at Bowling Green State University. An earlier version of these notes was available through my Web pages for some time and, judging from the e-mail Ive received, has found its way into the hands of more than a few readers around the world. Offering them in their current form seemed like the natural thing to do. Although my primary purpose for the course was to train one or two students to begin doing research in Banach space theory, I felt obliged to present the material as a series of compartmentalized topics, at least some of which might appeal to the nonspecialist. I managed to cover enough topics to suit my purposes and, in the end, assembled a reasonable survey of at least the rudimentary tricks of the trade. As a prerequisite, the students all had a two-semester course in real analysis that included abstract measure theory along with an introduction to functional analysis. While abstract measure theory is only truly needed in the final chapter, elementary facts from functional analysis, such as the HahnBanach theorem, the Open Mapping theorem, and so on, are needed throughout. Chapter 2, Preliminaries, offers a brief summary of several key ideas from functional analysis, but it is far from self-contained. This chapter also features a large set of exercises I used as the basis for additional review, when necessary. A modest background in topology is also helpful but, because many of my students needed review here, I included a brief appendix containing most of the essential facts. I make no claims of originality here. In fact, the presentation borrows heavily from several well-known sources. I tried my best to document these sources fully in the references and in the brief Notes and Remarks sections at the end of each chapter. You will also see that Ive included a few exercises to accompany each chapter. These only scratch the surface, of course. Energetic readers may want to seek out greater challenges through the readings suggested in the Notes and Remarks. My goal was a quick survey of what I perceive to be the major topics in classical Banach space theory: Basis theory, L p spaces, C(K) spaces, and a brief introduction to the geometry of Banach spaces. But the emphasis here is on classical; most of this material is more than thirty years old and, indeed, a great deal of it is more than fifty years old. Readers interested in contemporary research topics in Banach space theory are sure to be disappointed with this modest introduction and are encouraged to look elsewhere. Finally, I should point out that the course has proven to be of interest to more students than I had originally imagined. Basis theory, for example, has enjoyed a resurgence in certain modern arenas, and such chestnuts as the so-called gliding hump argument frequently resurface in a variety of contemporary research venues. From this point of view, the course has much to offer students interested in operator theory, frames and wavelets, and even in certain corners of algebra such as lattice theory. More important, at least from my point of view, is that the early history of Banach space theory is loaded with elegant, insightful arguments and clever techniques that are not only worthy of study in their own right but are also deserving of greater publicity. It is in this spirit that I offer these notes. Neal Carothers Bowling Green, Ohio February 2003 A Short Course on Banach Space Theory
标签: SHORT
