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
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
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
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
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