Development of Bioinformatic Tools for Virtual Cloning

虚拟克隆生物信息学工具的开发

• 批准号: 6583437
• 负责人: JEREMY A BRUENN
• 金额: $ 10万
• 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 2004-02-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6583437
• 关键词: artificial intelligence; biomedical automation; computer program /software; computer simulation; computer system design /evaluation; expression cloning; gene expression; genetic library; genetic manipulation; informatics; molecular biology information system; transfection /expression vector

DESCRIPTION (provided by applicant): The ability to delineate (at least in theory) all the proteins encoded in the human genome and all of those encoded by the genomes of major human parasites has given us an unprecedented opportunity to address the causes and treatment of every major human disease. However, the vast increase in biological knowledge that has resulted from the last decade of genomic DNA sequencing has led us to a a crisis in bioinformatics. This crisis is two-fold: analysis of data and planning of experiments. Most of the scientific 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. All modern experimental molecular biology (and, increasingly, structural biology) depends upon the availability of plasmid clones to address specific scientific questions. Although software facilitating DNA manipulations exists, few programs advise users of optimal strategies and none automate the process of clone generation. Genomics initiatives identify proteins at the genome level and demand the generation of hundreds of expression clones for recombinant protein production in exogenous hosts such as E. coli. Establishment of libraries of expression clones requires automation and optimization as well as effective means of data storage, archiving, annotation and query. To address these needs, as well as to facilitate routine DNA manipulations in virtually any molecular biology laboratory, we propose (1) to test and build a task centered virtual cloning expert system that serves as a knowledge base for DNA manipulations, and (2) to test and build an information automaton for the construction of expression clone libraries in support of structural genomics initiatives and other high throughput experiments.

描述（由申请人提供）：描述人类基因组中编码的所有蛋白质以及由主要人类寄生虫基因组编码的所有蛋白质的能力（至少在理论上），这给了我们前所未有的机会，可以解决每种主要人类疾病的原因和治疗。 然而，由于基因组DNA测序的最后十年，生物学知识的巨大增加使我们陷入了生物信息学的危机。 这场危机是两个方面：数据分析和实验计划。 在生物信息学中花费的大多数科学资源都花在数据分析工具上。尽管这些都是必不可少的，但我们不应忽略加速实际实验生物学进展的机会。 所有现代实验性分子生物学（以及越来越多的结构生物学）都取决于质粒克隆的可用性来解决特定的科学问题。 尽管存在促进DNA操作的软件，但很少有程序为用户提供最佳策略的建议，并且没有一个自动化的克隆生成过程。基因组学倡议在基因组水平上鉴定蛋白质，并要求产生数百个表达克隆，以在外源宿主（例如大肠杆菌）中产生重组蛋白质。 建立表达克隆库需要自动化和优化以及有效的数据存储，归档，注释和查询的方式。 为了满足这些需求，并促进几乎任何分子生物学实验室中的常规DNA操纵，我们建议（1）测试和建立一个以任务为中心的虚拟克隆专家系统，该系统是DNA操作的知识库，（2），以测试和构建一个信息自动化的信息，以通过支持结构基因组和其他较高的构建结构基因的培养物和其他构建较高的结构启动。