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：
8324569
负责人：
Kenneth Edward Rudd
金额：
$ 30.74万
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 2015-02-28
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8324569
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 Sequence 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 Genetic Transcription 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 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 quality assurance repaired satisfaction supercomputer tool web site

项目摘要

DESCRIPTION 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.

描述基因组尺度测序，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，并由基因的预测分析RNA支持以及使用计算机的蛋白质序列和结构。微生物基因组的平行发展科学，生物信息学，Internet 2.0和桌面超级计算机已帮助将这项革命带入学术，全球工业和政府实验室。但是，对此的准确和有效的管理大量新数据，使用专家策展监督来创建支持的可靠信息系统实验和系统生物学研究一直是一个持续的挑战。 ecogene.org证明了这一点可以使用开源工具构建高影响力，可靠的细菌基因组数据库在学术研究环境中的开销低。两个广泛的长期目标驱动ecogene.org 开发是：（1）可靠的非冗余数据库的准确，全面和及时交付统一的大肠杆菌K-12信息通过专家守门人审查，适合未来的基础跨学科研究，以及（2）通过其他细菌注释和研究项目的支持使用大肠杆菌作为模型系统开发的软件和方法。具体目的是：（1）收集和在控制输入数据流的质量时组织所有新发表的大肠杆菌研究结果提高界面功能，扩大ecogene.org的范围以包括所有大肠杆菌菌株，并提供具有ecogene.org的开源代码及其通用导数prokgene.org的公众；（2）带E。大肠杆菌K-12 MG1655 GenBank基因组信息每月以Ecogene.org充当一个每月最新的信息合作伙伴数据库和公众的功能，功能和引文更新建议的策展网关并扩大大肠杆菌K-12 GenBank记录中介绍的数据集和文档；（3）执行生物信息学研究（A）记录小蛋白的生物信息学验证和注释套件， SRNA，伪基因和5'UTR，并创建标准化的测试和训练集，以及（b）添加多种多样的统计算法成组合的模式搜索工具；（4）进行选定的实验室验证研究（a）解决包括信号肽/锚的蛋白质组验证中的注释差距和歧义性区分，脂蛋白和翻译开始（b）验证基因型/表型，并填补大的空白突变收集，（c）精确恢复实验室维护期间获得的突变，以恢复损失功能和表型。大肠杆菌基因组的准确注释本身就是必要的最了解的细胞生物。促进大肠杆菌K-12的持续研究也很重要提高我们对抗菌策略最重要的参考应变的理解细菌生物恐怖主义，并防止抗生素耐药性细菌流行病的威胁日益增加。

项目成果

期刊论文数量（8）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Bacterial genome reengineering.

细菌基因组重组。

DOI：
10.1007/978-1-61779-197-0_1
发表时间：
2011
期刊：
Methods in molecular biology (Clifton, N.J.)
影响因子：
0
作者：
Zhou,Jindan;Rudd,KennethE
通讯作者：
Rudd,KennethE

Small membrane proteins found by comparative genomics and ribosome binding site models.

DOI：
10.1111/j.1365-2958.2008.06495.x
发表时间：
2008-12
期刊：
Molecular microbiology
影响因子：
3.6
作者：
Hemm MR;Paul BJ;Schneider TD;Storz G;Rudd KE
通讯作者：
Rudd KE

EcoGene 3.0.

DOI：
10.1093/nar/gks1235
发表时间：
2013-01
期刊：
Nucleic acids research
影响因子：
14.9
作者：
Zhou J;Rudd KE
通讯作者：
Rudd KE

Structural analysis and mutant growth properties reveal distinctive enzymatic and cellular roles for the three major L-alanine transaminases of Escherichia coli.

DOI：
10.1371/journal.pone.0102139
发表时间：
2014
期刊：
PloS one
影响因子：
3.7
作者：
Peña-Soler E;Fernandez FJ;López-Estepa M;Garces F;Richardson AJ;Quintana JF;Rudd KE;Coll M;Vega MC
通讯作者：
Vega MC

Repression of small toxic protein synthesis by the Sib and OhsC small RNAs.

DOI：
10.1111/j.1365-2958.2008.06394.x
发表时间：
2008-12
期刊：
Molecular microbiology
影响因子：
3.6
作者：
Fozo EM;Kawano M;Fontaine F;Kaya Y;Mendieta KS;Jones KL;Ocampo A;Rudd KE;Storz G
通讯作者：
Storz G