Analysis and annotation of the E. coli genome sequence

大肠杆菌基因组序列的分析和注释

• 批准号: 7014514
• 负责人: Kenneth Edward Rudd
• 金额: $ 30.22万
• 依托单位: UNIVERSITY OF MIAMI SCHOOL OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2000
• 资助国家: 美国
• 起止时间: 2000-02-01 至 2008-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7014514
• 关键词: Escherichia coli; Escherichia coli k12; bacterial DNA; bacterial genetics; bioinformatics; biotechnology; data quality /integrity; functional /structural genomics; gene expression; genetic models; indexing; molecular biology information system; nucleic acid sequence; protein sequence; proteomics

DESCRIPTION (provided by applicant): Genome sequencing projects have provided a foundation for a new biology centered around the molecular representation of genes and proteins as sequences and structures in computers. The parallel development of genome science, bioinformatics, the Internet and desktop "supercomputers" has helped bring this revolution to academic, industry and government labs worldwide. Unfortunately, the adverse impact of database errors on experimental science is easily demonstrated. The broad, long-term objective of this proposal is to continue to improve the reliability of the genome and proteome sequences of the model organism Escherichia coli K-12, leading to a Gold Standard Reference Strain for prokaryotic organisms, especially Gram-negative pathogens. This proposal focuses on improving the accuracy of the E. coli genome and proteome. The specific aims are: (1) to ensure the continued maintenance, improvement and expansion of EcoGene, a primary data repository for the continually revised E. coli genome and proteome sequences, and their annotations; EcoGene also serves as the systematic ORF nomenclature registry for E. coli K-12. EcoGene is part of an annotation-sharing collaboration among the Coli Genetic Stock Center at Yale, the Colibri database at the Pasteur Institute, and SWISS-PROT; (2) to establish two Indexer positions for expert electronic and legacy journal surveillance, to ensure that newly published and pre-released functional data about E. coli genes is entered promptly and accurately into EcoGene, then released to the public, and partner databases; (3) to augment electronic data collection with bioinformatics analysis to (a) discover new evolutionary relationships, thus improving functional predictions and (b) detect-and-report internal and external database errors, including DNA and protein sequence errors, often detected and resolved during analysis-anomaly-refinement-reanalysis (AARR) cycles; and (4) to use laboratory studies to (a) resolve remaining DNA frameshift errors in the E. coli K-12 genome by re-sequencing, (b)verify ambiguous protein starts, and (c) verify the secreted (periplasmic and outer membrane) proteome. The accurate annotation of the E. coli genome is necessary in its own right as the most well-understood cellular organism, and to provide the foundation for the analysis of bacterial genomes whose characterizations will be crucial for the development of biological and chemical defense against bacterial bioterrorism.

描述（由申请人提供）：基因组测序项目为围绕基因和蛋白质的分子表示为计算机中的序列和结构的新生物学为基础。基因组科学，生物信息学，互联网和桌面的“超级计算机”的并行发展已将这项革命带入了全球学术，工业和政府实验室。不幸的是，很容易证明数据库错误对实验科学的不利影响。该提案的广泛长期目标是继续提高模型生物体大肠杆菌K-12的基因组和蛋白质组序列的可靠性，从而导致促性生物体（尤其是革兰氏阴性病原体）的金标准参考菌株。该提案的重点是提高大肠杆菌基因组和蛋白质组的准确性。具体目的是：（1）确保Ecogene的持续维护，改进和扩展，这是不断修订的大肠杆菌基因组和蛋白质组序列及其注释的主要数据存储库； Ecogene还充当大肠杆菌K-12的系统ORF命名注册表。 Ecogene是耶鲁大学大肠杆菌遗传储备中心，巴斯德研究所的Colibri数据库和瑞士 - 普罗特（Swiss-Prot）的一部分。 （2）为专家电子和旧版期刊监视建立两个索引职位，以确保将有关大肠杆菌基因的新发表和预发行的功能数据迅速准确地输入生态中，然后发布给公众，并将其发布给公众，以及合作伙伴数据库； （3）通过生物信息学分析来增强电子数据收集到（a）发现新的进化关系，从而改善功能预测，并检测内部和外部数据库误差，包括DNA和蛋白质序列错误，通常在分析过程中检测到和解决分析 - 分析 - 反对 - 重新结构分析（AARR）sidcles sycles sycles; （4）使用实验室研究来（a）通过重新测序来解决大肠杆菌K-12基因组中剩余的DNA递减错误，（b）验证歧义蛋白开始，并且（c）验证分泌的（骨膜和外膜和外膜）蛋白质组。大肠杆菌基因组的准确注释本身就是最受理解的细胞生物本身，并为分析细菌基因组的基础提供了基础，其特征对于开发针对细菌生物恐怖主义的生物学和化学防御至关重要。