An introduction to a tutorial on using the PhAnToMe (Phage Annotation Tools and Methods) website, databases (Phage SEED, Phage Metadata), and programs: phiRAST, PhageBioBIKE, and phiSIGNs

1. PhAnToMe Workshop Phage AnnotationTools and Methods 8/7/11 PhAnToMe Workshop-Evergreen 2011

2. Outline Demonstration: PhAnToMe project PhAnToMe website Phage SEED Vocabulary (PEGs, Subsystems, FIGfams) phiRAST Phage BioBIKE phiSIGNs Tutorial: Browse your favorite genome on SEED Check history and evidence, including similarities Align proteins Explore your phage coverage in metagenomes 8/7/11 PhAnToMe Workshop-Evergreen 2011

3. PhAnToMe Workshop Part IThe Phage SEED Database &The phiRAST Annotation Tool 8/7/11 PhAnToMe Workshop-Evergreen 2011

4. PhAnToMe: PHageANnotationTOols & MEthods NSF-funded project (2009-2012) Goals: Develop an infrastructure and new tools to generate automated, high-quality annotations of available phage sequences Develop 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 creatively Engage the insight of the research community to generate an even higher quality of annotation 8/7/11 PhAnToMe Workshop-Evergreen 2011

5. PhAnToMe: PHageANnotationTOols & MEthods NSF-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) 8/7/11 PhAnToMe Workshop-Evergreen 2011

6. The PhAnToMe website Main features: Tools Downloads PhAnToMers Links & Databases FAQs & News (Labs) 8/7/11 PhAnToMe Workshop-Evergreen 2011

7. The PhAnToMe website Some highlights: Tools > Phage SEED Tools > Phage Eco-Locator Tools > Phage metadata Tools > PhiSIGNs Community annotation tools Phage SEED > Adopt-a-phage Phage metadata > Phage lifestyle Downloads 8/7/11 PhAnToMe Workshop-Evergreen 2011

8. Phage SEED:Main concepts & vocabulary Protein-based database PEG = protein-encoding gene Functional role ≠ protein name The subsystems approach FIGfams: protein families based on sequence similarity chromosomal co-occurrence human curation 8/7/11 PhAnToMe Workshop-Evergreen 2011

9. 8/7/11 PhAnToMe Workshop-Evergreen 2011 What 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 subsystems Subsystems-basedannotation 8/7/11 PhAnToMe Workshop-Evergreen 2011

11. PhiRAST: automated annotation 8/7/11 PhAnToMe Workshop-Evergreen 2011

12. What do you need to annotate your genome? A sequenced genome Format: fasta or genbank (.gbk) A RAST username and password 8/7/11 PhAnToMe Workshop-Evergreen 2011

13. Audience survey Do you have a genome to annotate? Have you uploaded a genome to RAST? What specific requests you have for using SEED, RAST, etc.? 8/7/11 PhAnToMe Workshop-Evergreen 2011

14. RAST Demo by Karin Holmfeldt 8/7/11 PhAnToMe Workshop-Evergreen 2011

15. Additional Details 8/7/11 PhAnToMe Workshop-Evergreen 2011

16. PhAnToMe: PHageANnotationTOols & MEthods 8/7/11 PhAnToMe Workshop-Evergreen 2011

17. SEED vs. RAST vs. SEED Viewer 8/7/11 PhAnToMe Workshop-Evergreen 2011 SEED Viewer RAST New Genomes SEED Subsystems Editor Genomes Subsystems

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% similarity Also 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 annotations Creation of new subsystems or curation of new variants of existing subsystems increases number of functional roles that define FIGfams 8/7/11 PhAnToMe Workshop-Evergreen 2011

19. PhAnToMe Workshop Part IIPhage BioBIKE by Jeff Elhai et al. 8/7/11 PhAnToMe Workshop-Evergreen 2011

20. PhAnToMe Workshop Part IIIphiSIGNs by BhaktiDwivedi 8/7/11 PhAnToMe Workshop-Evergreen 2011

21. PhAnToMe Workshop Part IVHands-on Tutorial Ramy Aziz 8/7/11 PhAnToMe Workshop-Evergreen 2011

22. I. Browse your favorite genome 8/7/11 PhAnToMe Workshop-Evergreen 2011

23. II. Explore the protein page Annotation history Annotation clearinghouse Evidence similarities 8/7/11 PhAnToMe Workshop-Evergreen 2011

24. III. Aligning proteins (in context) Evidence> Similarities> Align Compare region, advanced settings 8/7/11 PhAnToMe Workshop-Evergreen 2011

25. IV. Explore your phage vs. metagenomes 8/7/11 PhAnToMe Workshop-Evergreen 2011