Collaborative Research: PHANTOME: Phage ANnotation TOols and MEthods

提案标题：合作研究：PHANTOME：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，这些病毒中的大多数是噬菌体，即感染细菌的病毒。噬菌体通过其多样化的生活方式和基因产物，在水平基因交换、构建天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的最致命毒素的基因，也可以携带给它们感染的宿主带来适应性优势的基因。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。可用的噬菌体基因组序列数量正在迅速增加；另一方面，它们代表了全球最大的未表征遗传物质储存库。解释这些数据所必需的生物信息学工具已经落后于基因组序列的增长。为噬菌体基因组分析开发平台和计算工具工具箱的拨款已被授予，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，亚利桑那大学生态和进化生物系。Elhai博士为副教授，其他三位研究员为助理教授。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，并从完全测序的噬菌体基因组和环境噬菌体宏基因组序列中注释噬菌体序列。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，通过熟悉的界面访问噬菌体基因组中包含的丰富信息。这些合作者制定了一项针对高中生、本科生和研究生的广泛而深远的教育计划。在使用这些工具方面接受培训的学生将通过用户论坛和研讨会轮岗成为培训师。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视图。国家科学基金会提案摘要提案：0850356 PI姓名：Edwards， robert打印自eJacket: 03/10/09第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