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1.
基于PC/Linux的核酸序列分析系统的构建及其应用   总被引:13,自引:2,他引:11       下载免费PDF全文
基于PC机和Linux操作系统, 利用Phred/Phrap/Consed软件和Blast软件, 构建了核酸序列大规模自动分析系统. 该套系统可自动完成从测序峰图向核酸序列的转化、载体序列去除、序列自动拼接、重复序列鉴定以及序列的相似性分析, 可加速对大规模测序数据的分析和利用.  相似文献
2.
新基因全长cDNA序列的获得常常是分子生物学工作者面临的难题。人类基因组计划及其相关计划的实施导致了大量表达序列标签(EST)的产生。利用一定的生物信息学算法,这些EST序列往往可用来对新基因片段进行延伸。采用Linux操作系统,利用Blast软件和Phrap软件以及EST数据库在微机上构建了EST序列的电子延伸系统,并对来自于人胎肝的11386条EST序列和511条插入片段全长cDNA序列进行了电子延伸,结果显示8373条EST序列和389条插入片段全长cDNA序列得到了程度不等的延伸,部分结果通过RACE实验得到证实。该套系统可高效地、规模化进行EST序列的延伸,可为通过实验获得新基因全长cDNA序列提供重要线索。 Abstract:Normally it is difficult to obtain full-length cDNA sequence of novel genes.More and more expressed sequence tags(ESTs) have been obtained since the start-up of human genome project.Powerful system is badly needed for data mining on these EST sequences.Based on a personal computer coupled with Linux operating system and EST database,the Blast software and Phrap software were used to construct a platform for in silico elongation of ESTs in our lab.The performance was tested using 11386 EST sequences and 511 partial-length cDNA sequences.Results demonstrated that 8373 EST and 389 cDNA sequence were elongated using this system.Thus the platform seems to be a fast way for full-length cDNA sequence cloning of new genes.  相似文献
3.
序列同源性分析软件Blast的WEB界面构建及其应用   总被引:5,自引:1,他引:4       下载免费PDF全文
基于局域网(Intranet)内的PC/Linux服务器, 构建了序列同源性分析软件Blast的WEB界面. 局域网内的所有计算机均可通过WEB方式访问该服务器进行公共数据库和自建数据库的查询,具有保密、高效、免费的优点,能够满足实验室和研究院所的大规模、快速数据分析任务.  相似文献
4.
基于Cygwin实现生物信息学软件从Unix/Linux向Windows移植   总被引:2,自引:0,他引:2  
Cygwin可在Windows环境下提供对Unix/Linux环境的模拟与支持,具有较为完善的Unix/Linux工具包和编程环境。利用Cygwin对常用的生物信息学数据分析软件如Sim4、FASTA、Phred/Phrap/RepeatMasker、EMBOSS、HMMER和ClustalW等进行重新编译,发现通过该方式能够获得可在Windows环境下运行的可执行代码,为利用Windows环境优势的同时进行跨平台生物信息学数据分析平台的开发提供重要参考价值。  相似文献
5.
基于Linux的cDNA文库序列分析平台的构建与应用   总被引:1,自引:0,他引:1  
本研究构建了基于Linux的cDNA文库序列分析平台,该分析平台可大批量自动处理测序后的序列,包括载体序列的去除、序列格式的转换、序列的自动拼接、序列对数据库的相似性搜索及全长ORF的预测等,可加速对大规模测序数据的分析和利用。用该平台对构建的野生大豆盐胁迫全长cDNA文库部分测序结果进行分析和利用。用该平台对构建的野生大豆盐胁迫全长cDNA文库部分测序结果进行分析,获得了较好的结果,已得到多个具有潜在价值的新基因序列。  相似文献
6.
The Linux cluster considered in this paper, formed from shuttle box XPC nodes with 2 GHz Athlon processors connected by dual Gb Ethernet switches, is relatively easily constructed, but, while effective as a throughput engine, may result in disappointing results when running explicitly parallel software if weakly-performing communication mechanisms and process spawning are selected. This paper carefully compares the implementations of communication and spawning primitives in MPICH-2, openMosix, and Linux Remote Procedure Call, forking, and various lower-level communication mechanisms. The test selection compares the provision of both a message-passing library, and a single system image software package, with direct use of lower-level primitives. The information in the paper will be of interest to those considering the use of one of the well-known packages, or directly writing their own distributed applications, or constructing a distributed language by layering on top of an existing set of parallel primitives. The results expose a ranking in terms of process spawning and a similar ranking of communication software performance. They reveal poor performance in certain circumstances, well below the hardware specification, which it is as well that the developer is aware of. In general, the paper emphasizes the importance of efficient transport software to cluster machines. David J. Johnston has worked as software engineer in research and development for 20 years, at ICL Ltd. and the Rutherford-Appleton Laboratory, UK. His strengths lie in generating and realizing algorithms for complex systems. His interests include languages and methodologies to shorten the software development process. He has recently completed a Ph.D. at the University of Essex, UK in position identification for augmented reality. He has co-authored a book on Computer Graphics. Martin Fleury is a Senior Lecturer at the University of Essex, UK, where he was also awarded a Ph.D. in Parallel Image Processing. His first degree was from Oxford University, and he holds an MSc in Astrophysics from the University of London. He is the principal author of a book on parallel computing for embedded systems. He has authored thirty-five journal papers in the last ten years on parallel image and vision processing, performance prediction, real-time systems, reconfigurable computing, software engineering, and video and document compression. Michael Lincoln has completed an M.Sc. and Ph.D. at the University of Essex, UK in the field of face recognition and face tracking. His work as a Senior Research Officer is concerned with radar control of aircraft landings. The cluster mentioned in the paper was constructed, configured, and commissioned by Michael. Andrew C. Downton was educated at Southampton University, UK, where he obtained a first class honours degree in Electronic Engineering in 1974, and a Ph.D. in 1982, and where he was also a lecturer. In 1995 he was promoted to a personal Chair at the University of Essex, UK, and in 1999 he became Head of the Department of Electronic Systems Engineering at Essex. His research interests include pattern recognition and image analysis; parallel computer architectures; hardware-software co-design; handwriting recognition; and document analysis. He is a Chartered Engineer and Fellow of the Institution of Electrical Engineers (IEE) and a Senior Member of the IEEE.  相似文献
7.
丁德武 《生物信息学》2012,10(3):151-153
对现实世界复杂网络的自相似性进行实证分析是当前该领域的一个热点问题。文章首先介绍了复杂网络自相似性的基本概念,随后阐述了自相似指数及其计算方法盒覆盖算法的基本原理和方法,最后对Linux与人类代谢这两种不同类型的复杂系统进行自相似性实证研究。研究结果表明,它们都是自相似的。  相似文献
8.
针对小型实验室特点和实际需要,提出并实现一个以服务器-客户机模式,涵盖web服务,生物序列分析,生物芯片数据分析,实验数据统计处理,文献服务等计算机辅助的通用解决方案。该解决方案已经应用在批量ESTs电子注释和寄生虫病分子诊断的靶序列筛选上。可作为小型实验室生物信息学基础设施部署。  相似文献
9.
The influences of the operating system and system-specific effects on application performance are increasingly important considerations in high performance computing. OS kernel measurement is key to understanding the performance influences and the interrelationship of system and user-level performance factors. The KTAU (Kernel TAU) methodology and Linux-based framework provides parallel kernel performance measurement from both a kernel-wide and process-centric perspective. The first characterizes overall aggregate kernel performance for the entire system. The second characterizes kernel performance when it runs in the context of a particular process. KTAU extends the TAU performance system with kernel-level monitoring, while leveraging TAU’s measurement and analysis capabilities. We explain the rational and motivations behind our approach, describe the KTAU design and implementation, and show working examples on multiple platforms demonstrating the versatility of KTAU in integrated system/application monitoring.
Alan MorrisEmail:
  相似文献
10.
The explosive growth of the bioinformatics field has led to a large amount of data and software applications publicly available as web resources. However, the lack of persistence of web references is a barrier to a comprehensive shared access. We conducted a study of the current availability and other features of primary bioinforo matics web resources (such as software tools and databases). The majority (95%) of the examined bioinformatics web resources were found running on UNIX/Linux operating systems, and the most widely used web server was found to be Apache (or Apache-related products). Of the overall 1,130 Uniform Resource Locators (URLs) examined, 91% were highly available (more than 90% of the time), while only 4% showed low accessibility (less than 50% of the time) during the survey. Furthermore, the most common URL failure modes are presented and analyzed.  相似文献
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