Collaborative Research: PHANTOME: Phage ANnotation TOols and MEthods

合作研究：PHANTOME：噬菌体注释工具和方法

• 批准号: 0850105
• 负责人: Matthew Sullivan
• 金额: $ 27.94万
• 依托单位: University of Arizona
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-04-15 至 2013-03-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0850105&HistoricalAwards=false
• 关键词: Collaborative; Research; PHANTOME; Phage; ANnotation

Proposal Title: Collaborative Research: PHANTOME: PHage ANnotation TOolsand MEthodsInstitution: San Diego State University FoundationAbstract Date: 03/09/09Viruses are the most abundant biological entities on the planet. Since the mostabundant living organisms on Earth are bacteria, the majority of these viruses arephages, the viruses which infect bacteria. Through their diverse lifestyles and geneproducts, phages play important roles in horizontal gene exchange, in structuringnatural microbial communities, and in global biogeochemical cycles. Phages carrygenes for some of the deadliest toxins known and can also carry genes which conferadaptive advantages to the hosts they infect. Furthermore, phage genes and theproteins they encode are the outcome of evolution over eons, the products of which wewould be able to exploit if only we could decode the information in the phage DNAsequences. The number of available phage genome sequences is increasing rapidly; onthe other hand, they represent the largest global reservoir of uncharacterized geneticmaterial. Bioinformatic tools necessary for interpreting this data has lagged behind thegrowth in genome sequences. Grants to develop a platform and toolbox ofcomputational tools for phage genome analysis have been awarded to supportcollaborative research in the laboratories of Drs. Robert Edwards, Department ofComputer Sciences, San Diego State University, Mya Breitbart, College of MarineSciences, University of South Florida, Jeffrey Elhai, Biology Department, VirginiaCommonwealth University and Matthew Sullivan, Department of Ecology andEvolutionary Biology, University of Arizona. Dr. Elhai is an Associate Professor, theother three investigators are Assistant Professors. This collaborative project is creatingnew computational tools to establish a consistent nomenclature for phage genomes, toannotate phage sequences, both from completely sequenced phage genomes and fromenvironmental phage metagenome sequences. Most importantly, this project willengage a wide spectrum of researchers, regardless of their computational background,to access the wealth of information contained in phage genomes through familiargraphical interfaces. These collaborators have developed an extensive and far-reachingeducation plan that targets high school students, undergraduate students and graduatestudents. The students trained in the use of the tools will rotate into trainer roles via userforums and workshops. The postdocs will be working across all the labs and therebygain an unparalleled panoramic view of phage biology.NATIONAL SCIENCE FOUNDATIONProposal AbstractProposal:0850356 PI Name:Edwards, RobertPrinted from eJacket: 03/10/09 Page 1 of 1

提案标题：合作研究：幻影：噬菌体注释工具和方法机构：圣地亚哥州立大学基金会摘要日期：03/09/09病毒是地球上最丰富的生物实体。由于地球上最丰富的生物体是细菌，因此这些病毒大多数是噬菌体，即感染细菌的病毒。通过其多样化的生活方式和基因产物，噬菌体在水平基因交换、构建自然微生物群落和全球生物地球化学循环中发挥着重要作用。噬菌体携带一些已知最致命毒素的基因，也可以携带赋予其感染的宿主适应性优势的基因。此外，噬菌体基因和它们编码的蛋白质是亿万年进化的结果，只要我们能够解码噬菌体 DNA 序列中的信息，我们就能够利用这些产物。可用噬菌体基因组序列的数量正在迅速增加；另一方面，它们代表了全球最大的未定性遗传物质库。解释这些数据所需的生物信息学工具已经落后于基因组序列的增长。已授予开发用于噬菌体基因组分析的计算工具平台和工具箱的赠款，以支持博士实验室的合作研究。 Robert Edwards，圣地亚哥州立大学计算机科学系，Mya Breitbart，南佛罗里达大学海洋科学学院，Jeffrey Elhai，弗吉尼亚联邦大学生物系，Matthew Sullivan，亚利桑那大学生态与进化生物学系。 Elhai博士是副教授，其他三名研究员是助理教授。该合作项目正在创建新的计算工具，以建立噬菌体基因组的一致命名法，注释来自完全测序的噬菌体基因组和环境噬菌体宏基因组序列的噬菌体序列。最重要的是，该项目将吸引广泛的研究人员，无论他们的计算背景如何，都可以通过熟悉的图形界面访问噬菌体基因组中包含的丰富信息。这些合作者制定了针对高中生、本科生和研究生的广泛而深远的教育计划。接受过工具使用培训的学生将通过用户论坛和研讨会轮流担任培训师角色。博士后将在所有实验室工作，从而获得噬菌体生物学无与伦比的全景。国家科学基金会提案摘要提案：0850356 PI 姓名：Edwards, Robert从 eJacket 打印：03/10/09 第 1 页，共 1 页