Collaborative Research: PHANTOME: PHage ANnotation TOols and MEthods

提案标题：合作研究：幻影组：噬菌体注释工具和方法机构：圣地亚哥州立大学成立摘要日期：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，这些病毒中的大多数是噬菌体，即感染细菌的病毒。通过其不同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。噬菌体携带已知的一些最致命毒素的基因，也可以携带赋予它们感染的宿主适应性优势的基因。此外，噬菌体基因及其编码的蛋白质是亿万年来进化的结果，如果我们能破译噬菌体DNA序列中的信息，我们就能利用这些产物。可用的噬菌体基因组序列的数量正在迅速增加；另一方面，它们代表着全球最大的未鉴定遗传物质的储藏库。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。为开发噬菌体基因组分析计算工具的平台和工具箱，已授予赠款，以支持以下实验室的合作研究：圣地亚哥州立大学计算机科学系Robert Edwards博士、南佛罗里达大学海洋科学学院Mya Breitbart博士、弗吉尼亚联邦大学生物系Jeffrey Elhai博士和亚利桑那大学生态与进化生物学系Matthew Sullivan博士。埃尔海博士是副教授，其他三名调查人员是助理教授。这个合作项目正在创建新的计算工具，以建立一个一致的噬菌体基因组命名，以注释噬菌体序列，从完全测序的噬菌体基因组和来自环境的噬菌体元基因组序列。最重要的是，这个项目将吸引广泛的研究人员，无论他们的计算背景如何，通过熟悉的图形界面访问包含在噬菌体基因组中的丰富信息。这些合作者制定了一项广泛而深远的教育计划，目标是高中生、本科生和研究生。接受工具使用培训的学生将通过用户论坛和讲习班轮流担任培训员。博士后们将在所有实验室工作，从而获得无与伦比的噬菌体生物学全景。自然科学基础建议摘要建议：0850356 PI姓名：爱德华兹，罗伯特从eJacket打印：03/10/09第1页，共1页

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