Development of Bioinformatic Tools for Virtual Cloning

虚拟克隆生物信息学工具的开发

• 批准号: 6788945
• 负责人: JEREMY A BRUENN
• 金额: $ 37.5万
• 依托单位: VIRMATICS, LLC
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-02-07 至 2006-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6788945
• 关键词: artificial intelligence; bioinformatics; biomedical automation; computer assisted sequence analysis; computer program /software; computer simulation; computer system design /evaluation; data management; experimental designs; expression cloning; genetic library; high throughput technology; molecular biology information system; molecular cloning

DESCRIPTION (provided by applicant): The elaboration of the sequences of the human genome and those of many cellular and viral parasites has given us an unprecedented opportunity to address the causes and treatment of every major human disease. It has also resulted in the formation of an entirely new field, bioinformatics, which promises to manage and analyze the vast amount of data being generated. Bioinformatics needs to supply tools for data analysis and tools for experimental design. Most of the scientific and corporate resources being expended in bioinformatics are being spent on data analysis tools. While these are essential, we should not neglect the opportunity to accelerate the progress of actual experimental biology. Essentially every experiment in biology now begins with cloning one or more pieces of DNA. Commercial software that facilitates virtual DNA cloning does exist, but it lacks any automation features and depends on primitive and/or fragmentary gene and vector databases. It is inadequate in planning the hundreds or thousands of clones necessary to address questions posed by the proteomics initiatives, because the lack of knowledge integration. In Phase I of this SBIR grant, we have built and tested a virtual cloning expert system, along with a very useful gene database and a uniquely annotated vector database that serve as a knowledge base for automated DNA manipulations. A collection of automated cloning modules and databases is now functional. In Phase II we will complete the virtual cloning expert system and develop a flexible platform for automated experimental design, data management and analysis. We will also construct a user database, improve the user interface and establish security protocols. The results will be a complete program suite as a stable and marketable product.

描述（由申请人提供）：人类基因组序列以及许多细胞和病毒寄生虫的序列的详细阐述为我们提供了前所未有的机会来解决每种主要人类疾病的原因和治疗。它还导致了一个全新领域的形成，即生物信息学，它有望管理和分析正在生成的大量数据。生物信息学需要提供数据分析工具和实验设计工具。在生物信息学上花费的大部分科学和企业资源都花在了数据分析工具上。虽然这些都是必不可少的，但我们不应忽视加速实际实验生物学进展的机会。现在，生物学中的每一项实验基本上都是从克隆一条或多条 DNA 开始的。促进虚拟 DNA 克隆的商业软件确实存在，但它缺乏任何自动化功能，并且依赖于原始和/或碎片基因和载体数据库。由于缺乏知识整合，它不足以规划解决蛋白质组学倡议提出的问题所需的数百或数千个克隆。在 SBIR 资助的第一阶段，我们构建并测试了一个虚拟克隆专家系统，以及一个非常有用的基因数据库和一个独特注释的载体数据库，可作为自动化 DNA 操作的知识库。自动克隆模块和数据库的集合现已投入使用。在第二阶段，我们将完成虚拟克隆专家系统，并开发一个用于自动化实验设计、数据管理和分析的灵活平台。我们还将构建用户数据库，改进用户界面并建立安全协议。结果将是一个完整的程序套件，作为稳定且适销对路的产品。