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（至少在理论上）人类基因组中编码的所有蛋白质以及主要人类寄生虫基因组中编码的所有蛋白质的能力为我们提供了前所未有的机会来解决以下问题的原因和治疗：人类的每一种重大疾病。 然而，过去十年基因组 DNA 测序带来的生物学知识的巨大增长给我们带来了生物信息学的危机。 这场危机有两个方面：数据分析和实验规划。 生物信息学上花费的大部分科学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。 所有现代实验分子生物学（以及越来越多的结构生物学）都依赖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，但很少有程序建议用户最佳策略，也没有程序自动执行克隆生成过程。基因组学计划在基因组水平上鉴定蛋白质，并需要生成数百个表达克隆，以便在大肠杆菌等外源宿主中生产重组蛋白质。 表达克隆库的建立需要自动化和优化，以及有效的数据存储、归档、注释和查询手段。 为了满足这些需求，并促进几乎所有分子生物学实验室的常规 DNA 操作，我们建议 (1) 测试和构建一个以任务为中心的虚拟克隆专家系统，作为 DNA 操作的知识库，以及 (2)测试和构建用于构建表达克隆库的信息自动机，以支持结构基因组学计划和其他高通量实验。