Introduction to PhAnToMe Workshop, 19th Evergreen Phage Meeting, 2011
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The document outlines the Phantome workshop held in 2011, focusing on phage annotation tools and methods for genome analysis. It describes the goals and outcomes of the NSF-funded Phantome project, including the development of annotation tools like Phage Seed and Phirast. The workshop also includes tutorials on using these tools and resources available for researchers studying phages.
Introduction to PhAnToMe Workshop, 19th Evergreen Phage Meeting, 2011
- 1. PhAnToMe WorkshopPhage AnnotationTools and Methods8/7/11PhAnToMe Workshop-Evergreen 2011
- 2. OutlineDemonstration:PhAnToMe projectPhAnToMe websitePhage SEEDVocabulary (PEGs, Subsystems, FIGfams)phiRASTPhage BioBIKEphiSIGNsTutorial:Browse your favorite genome on SEEDCheck history and evidence, including similaritiesAlign proteinsExplore your phage coverage in metagenomes8/7/11PhAnToMe Workshop-Evergreen 2011
- 3. PhAnToMe WorkshopPart IThe Phage SEED Database &The phiRAST Annotation Tool8/7/11PhAnToMe Workshop-Evergreen 2011
- 4. PhAnToMe: PHageANnotationTOols & MEthodsNSF-funded project (2009-2012)Goals:Develop an infrastructure and new tools to generate automated, high-quality annotations of available phage sequencesDevelop a resource through which the annotation and tools are made available to those who study phages in such a way that they can use them creativelyEngage the insight of the research community to generate an even higher quality of annotation8/7/11PhAnToMe Workshop-Evergreen 2011
- 5. PhAnToMe: PHageANnotationTOols & MEthodsNSF-funded project (2009-2012)Outcomes:PhAnToMe website/portal (http://www.phantome.org)Phage SEED (for already available phage genomes)PhiRAST (for user-uploaded phage genomes)Phage BioBIKE (Graphic programming interface to access phage SEED)8/7/11PhAnToMe Workshop-Evergreen 2011
- 6. The PhAnToMe websiteMain features:ToolsDownloadsPhAnToMersLinks & DatabasesFAQs & News(Labs)8/7/11PhAnToMe Workshop-Evergreen 2011
- 7. The PhAnToMe websiteSome highlights:Tools > Phage SEEDTools > Phage Eco-LocatorTools > Phage metadataTools > PhiSIGNsCommunity annotation toolsPhage SEED > Adopt-a-phagePhage metadata > Phage lifestyleDownloads8/7/11PhAnToMe Workshop-Evergreen 2011
- 8. Phage SEED:Main concepts & vocabularyProtein-based databasePEG = protein-encoding geneFunctional role ≠ protein nameThe subsystems approachFIGfams: protein families based onsequence similaritychromosomal co-occurrencehuman curation8/7/11PhAnToMe Workshop-Evergreen 2011
- 9. 8/7/11PhAnToMe Workshop-Evergreen 2011What is a subsystem? “A subset of functional roles studied across genomes” A spreadsheet where: each row represents a genome each column represents a functional role/ feature/ protein different patterns = variants
- 10. Advantages of subsystemsSubsystems-basedannotation8/7/11PhAnToMe Workshop-Evergreen 2011
- 11. PhiRAST: automated annotation8/7/11PhAnToMe Workshop-Evergreen 2011
- 12. What do you need to annotate your genome?A sequenced genomeFormat: fasta or genbank (.gbk)A RAST username and password8/7/11PhAnToMe Workshop-Evergreen 2011
- 13. Audience surveyDo you have a genome to annotate?Have you uploaded a genome to RAST?What specific requests you have for using SEED, RAST, etc.?8/7/11PhAnToMe Workshop-Evergreen 2011
- 14. RAST Demoby Karin Holmfeldt8/7/11PhAnToMe Workshop-Evergreen 2011
- 16. PhAnToMe: PHageANnotationTOols & MEthods8/7/11PhAnToMe Workshop-Evergreen 2011
- 17. SEED vs. RAST vs. SEED Viewer8/7/11PhAnToMe Workshop-Evergreen 2011SEED ViewerRASTNew GenomesSEEDSubsystems EditorGenomesSubsystems
- 18. What is a FIGfam?Set of proteins that play the same functional role as defined in a column of a curated subsystem and have ≥ 70% similarityAlso computed in closely related genomes from conserved sequence and proximity (functional clustering)Cluster-based, computed subsystems of unknown function are offered for exploration and assignment of function for continued improvement of FIGfam annotationsCreation of new subsystems or curation of new variants of existing subsystems increases number of functional roles that define FIGfams8/7/11PhAnToMe Workshop-Evergreen 2011
- 19. PhAnToMe WorkshopPart IIPhage BioBIKEby Jeff Elhai et al.8/7/11PhAnToMe Workshop-Evergreen 2011
- 20. PhAnToMe WorkshopPart IIIphiSIGNsby BhaktiDwivedi8/7/11PhAnToMe Workshop-Evergreen 2011
- 21. PhAnToMe WorkshopPart IVHands-on TutorialRamy Aziz8/7/11PhAnToMe Workshop-Evergreen 2011
- 22. I. Browse your favorite genome8/7/11PhAnToMe Workshop-Evergreen 2011
- 23. II. Explore the protein pageAnnotation historyAnnotation clearinghouseEvidencesimilarities8/7/11PhAnToMe Workshop-Evergreen 2011
- 24. III. Aligning proteins (in context)Evidence> Similarities> AlignCompare region, advanced settings8/7/11PhAnToMe Workshop-Evergreen 2011
- 25. IV. Explore your phage vs. metagenomes8/7/11PhAnToMe Workshop-Evergreen 2011