Collaborative Research: PHANTOME: PHage ANnotation TOols and MEthods

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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