质粒绘图软件PCircle的编制及Flash作为生物软件编制工具的可行性分析

以Flash作为软件编程工具 ,根据Flash在生物软件编制方面具有的优点 ,利用其优秀的图形图像处理能力与动作脚本语言 (ActionScript)相结合所具有的优势 ,编制了质粒绘图软件Pcircle。该软件克服了以往的质粒绘图软件在绘制图谱过程中不能随意修改操作的缺点 ,在绘制过程中 ,可在任意时候对生成的部件进行修改甚至删除。该软件已被生物软件网收录 ,供免费下载。同时详细分析了Flash作为生物软件编制工具所具有的优缺点 ,确定了作为生物软件编制工具的适用范围 ,可为Flash作为生物软件编制工具的使用起到指引作用。     

研发动态

中国烟草基因组数据库(1.0版)开放运行中国烟草基因组数据库(1.0版)近日面向行业开放运行。数据库设在国家烟草基因研究中心,储存了去年底绘制的绒毛状烟草和林烟草全基因组序列图谱的所有原始数据以及基因注释结果,总数据量将近7T。这两张序列图谱是目前已知植物基因组序列图谱中基因组最大、组装精度最高、组装     

MATLAB 7.X生物信息工具箱的应用———基因表达图谱分析（4）*

基因表达图谱原则上可了解整体细胞基因表达的信息,是基因组功能分析的重要研究手段。MATLAB 7.X生物信息工具箱为基因表达谱数据的分析和处理提供了一个综合环境,通过众多统计函数和绘图函数的结合使用,过滤不合格的基因数据和噪声数据,从而对基因表达数据进行聚类分析和主成分分析,绘制相关的基因表达图谱,完成基因芯片数据表达图谱的分析,分析结果可视化程度高,图表清晰、直观。本文主要以酿酒酵母Saccharomyces cerevisiae为例,详细描述了利用MATLAB 7.X生物信息工具箱对其基因表达图谱进行分析的过程。     

生物科技快讯

科学家绘制完成Ⅱ型糖尿病基因组图美国麻省理工学院(MIT)和哈佛大学Broad研究院、瑞典隆德(Lund)大学以及瑞士诺华公司(Novartis)的研究人员近日宣布．他们完成了基因组层面上的基因差异图谱．这些基因差异与Ⅱ型糖尿病等其他代谢疾病有密切关系。现在,科学家可以通过登录www．broad．mit．edu／diabetes／免费得到所有数据及分析结果。     

Java AWT和JAI技术在生物数据库图像显示上的应用

利用Java AWT和JAI技术绘制生物图像的方法可以使在实验室中得到的生物实验数据自动转化为需要的图谱,并且图像的精确度高。绘制成的图像既可以保存在本地硬盘中,也可以在浏览器中以网页的形式展示出来供研究人员分析使用。该方法目前已在上海生物信息技术研究中心开发的可视化工具MapViewer和主题数据库H2H,SRA中得到应用。     

滁菊的HPLC指纹图谱制作及其化学计量学分析

建立滁菊的HPLC指纹图谱,结合化学计量学手段对不同滁菊的指纹图谱进行分析研究,以期为滁菊的质量控制和产地追溯提供依据。采用HPLC法建立指纹图谱,并用中药色谱指纹图谱相似度评价系统(2012版)和系统聚类、主成分分析2种化学计量学法对指纹图谱和特征峰进行分析。分析结果发现样品有27个共有峰,12个滁菊样品具有较高的相似度,杭菊与滁菊的相似度较差,聚类分析与主成分分析结果和相似度分析结果一致。将HPLC指纹图谱与化学计量学结合可对滁菊进行鉴别和质量评价,为其质量控制和追溯提供了理论参考。     

介绍几种DNA的限制性内切酶图谱分析方法

限制性内切酶图谱(restriction map),又称物理图谱(physical map),是将各种限制性内切酶的切点在DNA上定位,绘制成的图谱(以下简称酶谱)。1968年Meselsen等人首先发现了限制性内切酶,至今已从四百多种菌株中分离了限制酶。1973年,Danna等绘制了SV40的简单图谱。此后各种DNA的酶谱不     

新版Tilia软件:中文指南和使用技巧*

Tilia软件一直是微体古生物学特别是孢粉学科使用最为普遍的一款专业计算机程序。该软件主要将样品数据经统计计算分析,将每个样品化石科属类型含量以图谱的形式依据地层深度或时间顺序排列显示,使化石数据转换为地层图式。基于各科属特别是优势或建群类型含量上下层位变化特点和规律,划分生物组合带,以图的形式直观解读生物群落的地史演替和环境变化等科学问题。由于此软件一直在英文语境下运行,功能多样,操作较为复杂,往往令国内初学者难以入手和深入。本文将以新版Tilia 2.0.45软件为对象,基于先期积累的使用经验,结合我国学者的思维方式,通过简单的孢粉数据实例,图解步骤和过程,力求通俗易懂。为此,推出"基础版"和"高阶版"两种使用说明以满足不同层次的人员需求,前者针对初学者旨在短时间内快速入门掌握孢粉百分比图谱制作的基本技巧,后者面向有一定操作经验学者力求在浓度图谱、通量图谱及"深度-年代"模型和Neotoma全球生态数据库等方面拓展提高。     

基于BP神经网络和RBF神经网络预测老年痴呆症疾病进展的对比研究

目的:比较反向传播算法(BP)神经网络和径向基函数(RBF)神经网络预测老年痴呆症疾病进展的效果。方法:以老年痴呆症随访数据为研究对象,以性别、年龄、受教育程度、有无高血压、有无高胆固醇、有无心脏病、有无中风史、有无家族史8个指标作为输入变量,以五年随访的MMSE差值为输出变量,构建基于BP神经网络和RBF神经网络的老年痴呆症疾病进展预测模型。结果:与BP神经网络模型相比,RBF神经网络预测的结果更好,能够有效地预测老年痴呆症疾病进展。结论:神经网络模型将老年痴呆症疾病进展预测问题转化为随访数据中相关测量指标与MMSE差值的非线性问题,为复杂的老年痴呆症疾病进展预测提供了新思路。     

介绍几种 DNA 的限制性内切酶图谱分析方法

限制性内切酶图谱(restriction map),又称物理图谱(physical map),是将各种限制性内切酶的切点在DNA上定位,绘制成的图谱(以下简称酶谱)。1968年Meselsen等人首先发现了限制性内切酶,至今已从四百多种菌株中分离了限制酶。1973年,Danna等绘制了SV40的简单图谱。此后各种DNA的酶谱不断被绘制。酶谱的出现,对DNA分子的克隆,基因定位,核酸序列的测定以及进化比较等方面的研究都有重要意义。DNA酶谱的分析方法很多,本文只简单叙述几种。一、双酶解分析方法此法是将酶两两组合进行彻底酶解,并与     

植物基因组比较作图研究进展

基因组比较作图是基因组研究的重要内容。植物比较作图研究表明,在长期的进化过程中,基因的组成表现出高度的保守性。随着植物遗传图谱和物理图谱的迅速发展,为植物比较作图奠定了重要的基础。现就植物基因组遗传图和物理图以及比较作图的最新研究进展作一介绍。     

植物细胞遗传图及其应用

细胞遗传图（cytogenetic map）综合了来自遗传图（genetic map）和细胞学图（cytological map）两方面的信息,它既能反映基因或DNA标记之间在染色体上的真实距离,又能显示它们与染色体的细胞学结构间确切的位置关系。构建植物细胞遗传图的宗旨是将遗传图上的诸多标记与其在染色体的具体位置联系起来。目前主要有两种方法用于细胞遗传图的构建。较广泛使用的一种方法是借助染色体断点来确定遗传标记在染色体上的位置,另一种方法是利用荧光原位杂交（FISH）直接把DNA序列定位到染色体上。此外,利用RN-cM图也可以把遗传标记定位于粗线期染色体。从细胞遗传图可以看出,染色体两臂的远端有较高的基因密度和重组频率。细胞遗传图在比较近缘植物基因组的同线性、揭示植物的进化关系、研究基因定位克隆等方面都有重要意义.     

Bovine chromosome 4 workshop: consensus and comprehensive linkage maps

The report of the bovine chromosome 4 (BTA4) workshop is presented. Six laboratories contributed a total of 30,168 informative meioses from 62 loci. Twenty-two loci were typed by at least two independent laboratories and were used to construct a consensus linkage map of BTA4. The remaining 40 loci were subsequently incorporated into a comprehensive map. The sex-averaged consensus map covered 131.4 cM. The female map was 124.3 cM in length, while the male map was 134.3 cM. The comprehensive sex-averaged map spanned 141.6 cM. The length of the female and male comprehensive maps were 123.1 cM and 156.4 cM, respectively. Average genetic distance between loci was 6 and 2.3 cM for the consensus and comprehensive linkage maps, respectively.     

A protocol for assessment and integration of vegetation maps,with an application to spatial data sets from south‐eastern Australia

Abstract Maps are important tools in natural resource management. Often, there may be multiple maps that represent the same resource, which have been constructed using very different philosophies and methods, at different scales, for different dates and areas. In such cases, conservation planners and other natural resource managers are faced with a choice of map that will best serve their decision making. However, the best available information for a given purpose is often a combination of data from a number of different source maps. In this paper we present a protocol for assessing and integrating multiple maps of vegetation for a particular area of interest. The protocol commences with a consideration of management or policy context and technical issues to determine the basic specifications for the map. It then defines and assesses a set of measurable attributes, representing the concepts of theme, accuracy, precision and currency, for all candidate maps available for compilation. The resulting ranks for accuracy, precision and currency are used to compute a suitability index, which is used to assemble a composite map from the most suitable candidate maps. The final step in the protocol is to display spatial patterns in thematic consistency, accuracy, precision and currency for the composite map. We demonstrate the application of the protocol by constructing a map that discriminates structurally intact native vegetation from cleared land for the whole of New South Wales, south‐eastern Australia. The source data include 46 maps that cover various parts of the region at various scales and which were made at different dates using different methods. The protocol is an explicit and systematic method to evaluate the strengths and weaknesses of alternative data sets. It implements spatial integration in a way that promotes overall accuracy, precision and currency of map data. It also promotes transparent reporting of map limitations, to help map users accommodate risks of map errors in their decision making, and to inform priorities for future survey and mapping.     

Comprehensive linkage map of bovine chromosome 27

The results of genotypic data contributed to the International Society for Animal Genetics (ISAG) Bovine Chromosome 27 Workshop are presented. Eight laboratories contributed 23 261 informative meioses from 44 loci. Eighteen loci were typed by at least two laboratories and were used to construct a consensus linkage map. Twenty-one loci were subsequently incorporated into a comprehensive map. The sex-averaged consensus map covered 66.9 cM. The sex-averaged comprehensive map was 75.5 cM, while the female and male maps were 73.1 and 63.7 cM, respectively. Five loci were excluded from the analysis because of ambiguous position in the linkage group and a low LOD score (less than 2.0). Average distance between loci in the comprehensive map was 1.98 cM.     

Comprehensive linkage map of bovine chromosome 11

The results of genotypic data contributed to the International Society of Animal Genetics (ISAG) Bovine Chromosome 11 (BTA11) Workshop are presented. Six laboratories contributed a total of 26 199 informative meioses from 80 loci. Thirty-six loci were typed by at least two independent laboratories and were used to construct a consensus linkage map of the chromosome. The remaining loci were subsequently incorporated into a comprehensive map. The sex-averaged consensus map covered 128.9 cM. The female consensus map was 101.2 cM, while the male consensus map was 129.8 cM. The comprehensive sex-averaged map was 134.2 cM and the average genetic distance between loci was 1.72 cM.     

Development of an in silico coding gene SNP map in pigs

A total of 5450 sequences obtained from the NCBI pig SNP database were consolidated into 465 unique sequences (189 singleton sequences and 276 contigs). These 465 sequences contained 1787 putative SNPs and had strong sequence homology to 433 human protein-coding genes based on blast analyses. These genes were assigned to the pig QTL maps ( http://www.animalgenome.org/QTLdb/pig.html ) via the human and pig comparative maps established by a pig radiation hybrid (RH) map. The SNP information characterized from this study provides a useful functional gene variation resource to facilitate QTL data mining in the pig genome.     

Mapping a new frontier; development of integrated cytogenetic maps in plants

Cytogenetic maps, as the name implies, incorporate data from genetic maps with actual cytological features of chromosomes such as centromeres, knobs and, recently, fluorescence in situ hybridization (FISH) signals. Integration of genetic and cytological maps has been accomplished primarily in two ways. The first general strategy is to create a chromosome breakpoint, then determine its cytological position using microscopy, and its position on the genetic map using genetic techniques. A second strategy is by the direct hybridization of genetically mapped sequences onto chromosomes by FISH. The aim of this review is to provide an overview of the state of this field in plants. We review the history and uses of cytogenetic maps, and discuss future directions based on what we have learned. Electronic Publication     

Chromosomal assignment of chicken clone contigs by extending the consensus linkage map

The bacterial artificial clone-based physical map for chicken plays an important role in the integration of the consensus linkage map and the whole-genome shotgun sequence. It also provides a valuable resource for clone selection within applications such as fluorescent in situ hybridization and positional cloning. However, a substantial number of clone contigs have not yet been assigned to a chromosomal location or have an ambiguous chromosome assignment. In this study, 86 single nucleotide polymorphism markers derived from 86 clones were mapped on the genetic map. These markers added anchoring information for 56 clone contigs and 13 individual clones, covering a total of 57,145 clones.     

A human-horse comparative map based on equine BAC end sequences

In an effort to increase the density of sequence-based markers for the horse genome we generated 9473 BAC end sequences (BESs) from the CHORI-241 BAC library with an average read length of 677 bp. BLASTN searches with the BESs revealed 4036 meaningful hits (E 相似文献