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首页> 外文学位 >A genomic approach to splice variant detection, primer design, and identification of gene trap sequence tags.
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A genomic approach to splice variant detection, primer design, and identification of gene trap sequence tags.

机译：用于剪接变体检测，引物设计和基因陷阱序列标签识别的基因组方法。

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摘要

The availability of full genome sequences for many organisms has greatly increased the reach of bioinformatics. In my research, I have used a variety of techniques to leverage the information carried in mouse, human, and viral genomes to address a diverse set of challenges.; One challenge was to devise a set of sequences to detect various strains of Human Papillomavirus (HPV). Chapter I describes the method by which I designed probe sequences common to multiple genomes to efficiently isolate HPV DNA from human tissue samples and probe sequences unique to each HPV genome to differentiate between viral strains for the purpose of diagnosing infections.; Chapter II depicts my role in developing the prototype International Gene Trap Consortium web resource, which presents information about embryonic stem cell lines carrying single gene knockouts to the public. Much of this work involved the creation of a new web site and a multi-path process for identification of gene trap sequence tags. Chapter III describes work that developed out of the transition from an mRNA transcript-based sequence tag annotation method to a process that combines transcript matching with localization to the mouse genome. To understand better the localization of gene trap sequence tags to the mouse genome, I compared stand-alone versions of the common genome alignment programs BLAT, SSAHA, and MegaBLAST.; Chapter IV details a method to detect splice variation in different tissues. I developed a process to combine information about splice variants gained by aligning expressed-sequence tags (ESTs) with full-length gene transcripts with microarray analysis to detect splice variants in high-throughput expression data. This method utilized data from pre-existing microarray expression experiments, and so had the potential for large-scale academic and industry use.
机译：许多生物体的完整基因组序列的可用性大大增加了生物信息学的范围。在我的研究中，我使用了多种技术来利用小鼠，人类和病毒基因组中携带的信息来应对各种挑战。一个挑战是设计一套序列来检测人类乳头瘤病毒（HPV）的各种菌株。第一章描述了我设计多个基因组共有的探针序列以从人组织样本中有效分离HPV DNA的方法，以及每个HPV基因组独特的探针序列以区分病毒株以诊断感染的方法。第二章描述了我在开发国际基因陷阱联盟原型网络资源中的角色，该资源向公众介绍了携带单基因敲除的胚胎干细胞系的信息。这项工作大部分涉及创建新的网站和用于识别基因陷阱序列标签的多路径过程。第三章介绍了从基于mRNA转录物的序列标签注释方法过渡到结合转录物匹配和小鼠基因组定位的过程的工作。为了更好地了解基因陷阱序列标签在小鼠基因组中的定位，我比较了通用基因组比对程序BLAT，SSAHA和MegaBLAST的独立版本。第四章详细介绍了一种检测不同组织中剪接变异的方法。我开发了一种程序，该程序将通过将表达序列标签（EST）与全长基因转录物比对而获得的剪接变体信息与微阵列分析相结合，以检测高通量表达数据中的剪接变体。这种方法利用了已有的微阵列表达实验中的数据，因此具有大规模学术和工业用途的潜力。

著录项

  • 作者

    Harper, Courtney.;

  • 作者单位

    University of California, San Francisco.$bBiological and Medical Informatics.;

  • 授予单位 University of California, San Francisco.$bBiological and Medical Informatics.;
  • 学科 Biology Bioinformatics.
  • 学位 Ph.D.
  • 年度 2007
  • 页码 119 p.
  • 总页数 119
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

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