A GENTLE INTRODUCTION TO SNP ANALYSIS: RESOURCES AND TOOLS

JAMES T. L. MAH; K. S. CHIA

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A GENTLE INTRODUCTION TO SNP ANALYSIS: RESOURCES AND TOOLS

机译：SNP分析的简要介绍：资源和工具

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Bioinformatics is the use of informatics tools and techniques in the study of molecular biology, genetic, or clinical data. The field of bioinformatics has expanded tremendously to cope with the large expansion of information generated by the mouse and human genome projects, as newer generations of computers that are much more powerful have emerged in the commercial market. It is now possible to employ the computing hardware and software at hand to generate novel methodologies in order to link data across the different databanks generated by these international projects and derive clinical and biological relevance from all of the information gathered. The ultimate goal would be to develop a computer program that can provide information correlating genes, their single nucleotide polymorphisms (SNPs), and the possible structural and functional effects on the encoded proteins with relation to known information on complex diseases with great ease and speed. Here, the recent developments of available software methods to analyze SNPs in relation to complex diseases are reviewed with emphasis on the type of predictions on protein structure and functions that can be made. The need for further development of comprehensive bioinformatics tools that can cope with information generated by the genomics communities is emphasized.

机译：生物信息学是在分子生物学，遗传学或临床数据研究中使用信息学工具和技术的方法。随着商业市场上出现了功能更强大的新一代计算机，生物信息学领域已得到极大扩展，以应对由鼠标和人类基因组计划生成的信息的大量扩展。现在可以使用手头的计算硬件和软件来生成新颖的方法，以便跨这些国际项目生成的不同数据库之间的数据链接，并从收集的所有信息中得出临床和生物学相关性。最终目标是开发一种计算机程序，可以轻松，快速地提供与基因，单核苷酸多态性（SNPs）相关的信息，以及与复杂疾病的已知信息相关的编码蛋白质可能的结构和功能作用。在此，回顾了分析与复杂疾病相关的SNP的可用软件方法的最新进展，重点是对蛋白质结构和功能的预测类型。强调需要进一步开发能够应对基因组学社区所产生信息的综合生物信息学工具。

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《Journal of Bioinformatics and Computational Biology》 |2007年第5期|共16页
作者
JAMES T. L. MAH; K. S. CHIA;
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正文语种 eng
中图分类细胞生物学;
关键词
Single nucleotide polymorphism; complex disease; nonsynonymous;

机译：单核苷酸多态性;复杂疾病;非同义;

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1. A GENTLE INTRODUCTION TO SNP ANALYSIS: RESOURCES AND TOOLS [J] . JAMES T. L. MAH, K. S. CHIA Journal of Bioinformatics and Computational Biology . 2007,第5期

机译：SNP分析的简要介绍：资源和工具
2. Tools for Analysis and Design of Distributed Resources—Part II: Tools for Planning, Analysis and Design of Distribution Networks With Distributed Resources [J] . Martinez J. A., de Leon F., Mehrizi-Sani A., Power Delivery, IEEE Transactions on . 2011,第3期

机译：分布式资源分析和设计工具第二部分：具有分布式资源的分配网络的规划，分析和设计工具
3. SNP2RFLP: a computational tool to facilitate genetic mapping using benchtop analysis of SNPs [J] . Wesley A. Beckstead, Bryan C. Bjork, Rolf W. Stottmann, Mammalian Genome . 2008,第10a12期

机译：SNP2RFLP：使用台式SNP分析方便遗传图谱的计算工具
4. A general workflow for differential expression analysis of RNA-seq and introductions on related tools [C] . Zhong Zhang International Conference on Electrical Electronics Engineering and Computer Science . 2016

机译：RNA-SEQ差异表达分析的一般工作流程及相关工具的介绍
5. Gentle introduction resource--Digital humanities web application. [D] . Evans, James Anderson Laird. 2014

机译：柔和的介绍资源-数字人文Web应用程序。
6. A Gentle Introduction to Bayesian Analysis: Applications to Developmental Research [O] . Rens van de Schoot, David Kaplan, Jaap Denissen, -1

机译：贝叶斯分析的温和介绍：在发展研究中的应用
7. : "This paper deals with the functionality of the flaked stone assemblages from several Neolithic sites of the NE of the Iberian Peninsula. The chronological framework ranges from the mid-6th to the mid-4th millennium cal. BCE, which corresponds to the Early and Middle Neolithic. This long period ranges from the arrival of the first farming communities in the Iberian Peninsula, around 5600-5500 cal. BCE, to 3600-3500 cal. BCE, two millennia later, when Neolithic communities had stably occupied most of the available territory, from the mountainous areas of the Pyrenees to the coastal areas of the Mediterranean.In this context, the NE of the Iberian Peninsula is one of the areas where a major number of use-wear analyses have been carried out, especially for what concerns the Neolithic period. This is mainly due to the interest shown by the directors of the excavations and by the Spanish use-wear specialists as well; both participated and cooperated in order to enlarge the number of contexts studied, making the NE of the Iberian Peninsula one of the areas of Europe with the largest number of ‘functional studies’. As a result, today we have a reliable picture of the type of lithic tools used by the first farming groups, how they were used, and which needs they were satisfying.The methodology employed for this type of analysis is today broadly shared by most use-wear specialists. A stereoscopic microscope is used together with a reflected-light microscope for the analysis of the archaeological specimens. Afterwards, the observed use-wear traces are compared with the traces from experimental tools. This study primarily made use of the tools preserved at the ‘Traceoteque’ of the Institución Milà y Fontanals of the CSIC of Barcelona.This paper presents the results obtained for the different types of analysed sites and the relative lithic assemblages. In this way, tools from different contexts are compared: open-air sites, caves and rock-shelters, pit-sites, burials, and mining sites. Such a diversity of contexts allowed for the exploration of the existence of recurrences and differences in the functionality of the lithic tools from one site to another. The results obtained have also provided information on some aspects related to the economic processes carried out at the different sites, caves, rock-shelters and open-air contexts. It has been possible to gain fresh data on the types of tasks carried out and their relative importance for each site, their relation with the geographical and environmental context and the natural resources available there. In addition, analysing tools recovered from burials – mainly individual inhumations – provided information on the relationships between the buried individuals and the working tools, in particular exploring the relationships between sex and age patterns and the types of tools deposited as goods.In conclusion, use-wear analysis allowed for the exploration of a variety of issues; from technical aspects related to the production and management of the lithic resources to social aspects related to the subsistence activities and the individuals that carried them out." [O] . Gibaja Bao, Juan Francisco, Mazzucco, Niccolo 2015

机译：：“本文研究了伊比利亚半岛东北部几个新石器时代遗址的片状石材组合的功能。时间框架从公元前6世纪中叶到4世纪中叶，分别对应于早期和早期。新石器时代中期，这段时间的长短是从伊比利亚半岛的第一个农业社区到来，大约在公元前5600-5500 cal，到了两千年后的3600-3500 BCE，当时新石器时代的社区稳定地占据了大部分可用土地。从比利牛斯山脉山区到地中海沿岸地区。在这种情况下，伊比利亚半岛东北部是进行过大量使用磨损分析的地区之一，尤其是在关注方面新石器时代，这主要是由于发掘负责人和西班牙使用服装专家表现出的浓厚兴趣；他们参与和合作以扩大孔蒂的数量xts进行了研究，使伊比利亚半岛的NE成为“功能研究”数量最多的欧洲地区之一。结果，今天我们可以可靠地了解第一批耕作小组使用的石器工具的类型，使用方法以及它们满足的需求。今天，大多数使用方法广泛共享用于这种类型的分析的方法穿专家。立体显微镜与反射光显微镜一起用于分析考古样本。然后，将观察到的使用磨损痕迹与实验工具的痕迹进行比较。这项研究主要利用了巴塞罗那CSIC的米拉·丰塔纳尔研究所的“ Traceoteque”中保存的工具。本文介绍了针对不同类型的分析地点和相对石器组合所获得的结果。通过这种方式，可以比较来自不同环境的工具：露天场所，洞穴和岩石避难所，露天场所，埋葬场所和采矿场所。如此多样的上下文允许探索重复性的存在以及从一个站点到另一个站点的石器工具的功能差异。所获得的结果还提供了与在不同地点，洞穴，避难所和露天环境中进行的经济过程有关的某些方面的信息。可以获得有关所执行任务的类型及其对每个站点的相对重要性，它们与地理和环境环境以及那里可用自然资源的关系的新数据。此外，对从墓葬中回收的工具（主要是个人遗体）进行分析，可提供有关被掩埋的个体与工作工具之间关系的信息，尤其是探索性别与年龄模式之间的关系以及作为商品存放的工具的类型。磨损分析允许探索各种问题；从与石器资源的生产和管理有关的技术方面到与自给活动及其实施者有关的社会方面。”

A GENTLE INTRODUCTION TO SNP ANALYSIS: RESOURCES AND TOOLS

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