Analysis and annotation of the E. coli genome sequence

大肠杆菌基因组序列的分析和注释

基本信息

批准号：
7737676
负责人：
Kenneth Edward Rudd
金额：
$ 31.37万
依托单位：
UNIVERSITY OF MIAMI SCHOOL OF MEDICINE
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-09-30 至 2013-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7737676
关键词：
Algorithms Amino Acid Sequence Anti-Bacterial Agents Bacterial Antibiotic Resistance Bacterial Genome Bioinformatics Biological Biological Models Biology Biotechnology Cells Classification Code Collaborations Collection Communities Community Services Computer software Computers DNA Data Data Set Database Management Systems Databases Development Discipline Discrimination Documentation Environment Epidemic Escherichia coli Floods Foundations Friends Future Gatekeeping Gel Genbank Generic Drugs Genes Genetic Genome Genome engineering Genomics Genotype Goals Gold Grant Information Systems Interdisciplinary Study Internet Laboratories Life Link Lipoproteins Maintenance Maps Masks Methods Microbial Genome Sequencing Microbiology Modeling Molecular Mutation Nationalities Organism Pattern Pattern Recognition Peptide Sequence Determination Peptide Signal Sequences Phenotype Procedures Proteins Proteome Proteomics Pseudogenes Publications Publishing Quality Control RNA RNA Sequences Records Reference Standards Research Research Project Grants Research Training Resources Restriction Mapping Retrieval Route Science Scientist Source Source Code Stream Structure Students Suggestion Systems Biology Terrorism Testing Time Training Translations Untranslated Regions Update Validation Work Writing base design flexibility functional restoration genome database genome sequencing improved innovation interest man microbial genome mutant novel open source peer protein expression prototype public health relevance quality assurance repaired satisfaction supercomputer tool web site

项目摘要

DESCRIPTION (provided by applicant): Genome-scale sequencing, RNA and protein expression studies, and systematic functional characterization projects have provided a foundation for a new microbiology, supported by predictive analysis of gene, RNA and protein sequences and structures using computers. The parallel development of microbial genome science, bioinformatics, Internet 2.0 and desktop supercomputers has helped bring this revolution to academic, industrial and governmental laboratories worldwide. However, the accurate and efficient management of this flood of new data, using expert curatorial oversight to create reliable information systems supporting experimental and systems biology research, has been an ongoing challenge. EcoGene.org demonstrates that a high impact, reliable bacterial genome database can be constructed with open source tools and maintained with low overhead in an academic research environment. Two broad, long-term objectives drive EcoGene.org development are: (1) the accurate, comprehensive and timely delivery of reliable non-redundant database- unified E. coli K-12 information vetted through an expert gatekeeper and suitable as a foundation for future interdisciplinary research, and (2) the support of other bacterial annotation and research projects through software and methods developed using E. coli as a model system. The specific aims are: (1) to collect and organize all newly published E. coli research results while controlling the quality of the input data streams, to improve interface functionality, to expand the scope of EcoGene.org to include all E. coli strains, and to provide the public with open source code for EcoGene.org and its generic derivative ProkGene.org; (2) to bring the E. coli K-12 MG1655 Genbank genome information up-to-date on a monthly basis with EcoGene.org acting as a curatorial gateway for feature, function and citation update suggestions from partner databases and the public and to expand the datasets and documentation presented in the E. coli K-12 GenBank record; (3) to perform bioinformatics research (a) to document bioinformatics validation and annotation suites for small proteins, sRNAs, pseudogenes and 5' UTRs, and to create standardized test and training sets, and (b) to add diverse statistical algorithms into a combined pattern search tool; (4) to perform selected laboratory verification studies to (a) resolve annotation gaps and ambiguities in proteome verifications including signal peptide/anchor discriminations, lipoproteins, and translation starts (b) verify the genotypes/phenotypes and fill gaps in large mutant collections, and (c) precisely revert mutations acquired during laboratory maintenance to restore lost functions and phenotypes. The accurate annotation of the E. coli genome is necessary in its own right as the most well understood cellular organism. It is also important to facilitate continued research on E. coli K-12 to increase our understanding of the reference strain most critical for anti-bacterial strategies to defend against bacterial bio-terrorism and to protect against the increasing threat of antibiotic-resistant bacterial epidemics. PUBLIC HEALTH RELEVANCE: EcoGene.org is a web site for scientists interested in the biology of Escherichia coli K-12. Even before genomes began to be sequenced, we knew more about the life of E. coli than any other organism. Now that we have all of the genes for E. coli, we have the possibility of attaining a nearly complete understanding of how a cell works in minute detail. The wealth of information collected at EcoGene.org from all over the world about the life of E. coli, both friend and foe of man, should help in achieving this

描述（由申请人提供）：基因组规模测序，RNA和蛋白质表达研究以及系统的功能表征项目为新的微生物学提供了基础，并通过使用计算机对基因，RNA和蛋白质序列和结构进行了预测分析。微生物基因组科学，生物信息学，Internet 2.0和桌面超级计算机的并行发展有助于将这项革命带入了全球学术，工业和政府实验室。但是，使用专家策展监督来创建支持实验和系统生物学研究的可靠信息系统的准确和有效管理一直是一个持续的挑战。 ecogene.org表明，可以使用开源工具来构建高影响，可靠的细菌基因组数据库，并在学术研究环境中保持低开销。两个广泛的长期目标推动Ecogene.org的发展是：（1）通过专家守护者审查的可靠的非冗余数据库的准确，全面和及时提供可靠的非冗余数据库 - 统一的E. Coli K-12信息，并适合将未来的跨学科研究基础，以及（2）通过使用软件和方法的其他细菌的支持和方法来支持E. coli and coli and coli and coli and coli and coli and coli and coli a coli and coli a coli a coli and a coli a coli and coli。具体目的是：（1）在控制输入数据流的质量，提高界面功能，扩大ecogene.org的范围以包括所有大肠杆菌菌株，并为公众提供Ecogene.org及其通用的衍生物Prokgene.org; （2）将大肠杆菌K-12 MG1655 GenBank基因组信息每月使用Ecogene.org每月最新，充当合作伙伴数据库和公众的功能，功能和引用更新建议的策展网关，并扩展了E. Coli K-12 GenBank记录中的数据集和文档；（3）进行生物信息学研究（a）以记录针对小蛋白质，srNA，伪基因和5'UTR的生物信息学验证和注释套件，并创建标准化的测试和训练集，以及（b）将多样的统计算法添加到合并的模式搜索工具中；（4）对（a）进行选定的实验室验证研究解决蛋白质组验证中的注释差距和歧义性，包括信号肽/锚固区分，脂蛋白和翻译开始（b）验证大型突变集合中的基因型/表型和填充差距，以及（c）精确恢复的突变及其在实验室中均可恢复。大肠杆菌基因组的准确注释本身是必不可少的，这是最知名的细胞生物。促进对大肠杆菌K-12的持续研究也很重要，以提高我们对抗菌策略最重要的参考菌株的理解，以防御细菌生物 - 恐怖主义，并防止抗抗生素耐药细菌的威胁日益增加。公共卫生相关性：Ecogene.org是一个网站，供对大肠杆菌K-12生物学感兴趣的科学家。甚至在基因组开始进行测序之前，我们对大肠杆菌的生命的了解要比任何其他生物都多。现在，我们拥有大肠杆菌的所有基因，我们有可能几乎完全了解细胞的细节工作方式。来自世界各地的ecogene.org收集的大量信息，关于大肠杆菌的生活，包括人的朋友和敌人，都应该有助于实现这一目标