The Opera of Phantome - 2016 (presented at the EMBO Viruses of Microbes 2016 meeting)
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Tools and Methods developed under the PhAnToMe (http://www.phantome.org) project between 2009-2012—and updated in 2015. The tools and database rely on the Subsystems Technology, the SEED (http://theseed.org) environment, and RAST server (http://rast.nmpdr.org) This is the fifth such presentation; this year at the EMBO Viruses of Microbes 2016 Meeting, 21 July 2016 (http://events.embo.org/16-virus-microbe)
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The Opera of Phantome - 2016 (presented at the EMBO Viruses of Microbes 2016 meeting)
- 1. The Opera of PhAnToMe 2016 Ramy K. Aziz (@azizrk) July 21 2016 opus (LT) = work (Pl. opera) SEED-based phage database (2009-2013-…) Phage Genomics Workshop, VoM 2016 giantmicrobes.com
- 2. 21 July 2016 History Phage Genomics - VoM 2016 NSF-funded, 3-year project (09- 12) to develop Phage Annotation Tools and Methods Four Centers: - SDSU, San Diego, CA - VCU, Richmond, VA - USF, St. Pete FL - UA, Tucson, AZ
- 3. http://www.phantome.org 21 July 2016 Web portal Phage Genomics - VoM 2016
- 4. I. THE ENVIRONMENT The Opera of PhAnToMe 2.0 Phage Genomics - VoM 2016
- 5. I. The Environment: SEED http://theseed.org 21 July 2016 Aziz RK,, et al. (2012) PLoS ONE 7(10): e48053. doi:10.1371/journal.pone.0048053 Phage Genomics - VoM 2016
- 6. SEED: Main concept One genome All genomes 21 July 2016 Phage Genomics - VoM 2016
- 7. SEED: Main concept One genome All genomes 21 July 2016 Phage Genomics - VoM 2016 “Subsystems-based technologies were developed in the SEED with the view that the interpretation of one genome can be made more efficient and consistent if hundreds of genomes are simultaneously annotated in one subsystem at a time”
- 8. SEED: Main concept • Protein-based database Jargon: PEG = protein-encoding gene • The subsystems approach and • FIGfams: protein families based on – sequence similarity – chromosomal co-occurrence, gene order, synteny – human curation, evidence-based expert assertions 21 July 2016 Phage Genomics - VoM 2016
- 9. RAST: automated annotation 21 July 2016 Phage Genomics - VoM 2016
- 10. 21 July 2016 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 Function 1 Function 2 … Function n Genome a Genome b … Genome z Phage Genomics - VoM 2016
- 11. II. THE TOOLBOX The Opera of PhAnToMe 2.0 Phage Genomics - VoM 2016
- 12. II. PhAnToMe ToolBox http://www.phantome.org 21 July 2016 Phage Genomics - VoM 2016
- 13. The ToolBox: The RAST family • (At least) Five ways to annotate a genome via RAST: – RAST (http://rast.nmpdr.org) • annotates online, saves your genome on server – myRAST (local) • uses the server but you can edit offline) – “PhAST” (http://www.phantome.org/PhageSeed/Phage.cgi?page=phast) • phage-optimized gene-calling – Use your favorite gene caller then upload gbk file to RAST – RASTtk (second-generation RAST) • modular • batch upload 21 July 2016 Phage Genomics - VoM 2016
- 14. http://rast.nmpdr.org 21 July 2016 Phage Genomics - VoM 2016
- 15. http://rast.nmpdr.org 21 July 2016 Phage Genomics - VoM 2016
- 16. “PhAST”: phage-optimized RAST 21 July 2016 Phage Genomics - VoM 2016 http://www.phantome.org/PhageSeed/Phage.cgi?page=phast
- 17. “PhAST”: phage-optimized RAST 21 July 2016 Phage Genomics - VoM 2016 http://www.phantome.org/PhageSeed/Phage.cgi?page=phast
- 18. RASTtk (RAST toolkit) 21 July 2016 Phage Genomics - VoM 2016
- 19. RASTtk (RAST toolkit) 21 July 2016 Phage Genomics - VoM 2016
- 20. The RASTtk Microbial Annotation Pipeline FASTA QC FASTA to Genome TO Call rRNAs Call tRNAs Call CDSs Prodigal Call CDSs Glimmer3 Annotate Proteins K-mer v2 Annotate Proteins K-mer v1 Call CRISPRs CALL Phages (PhiSpy) Find Repeats Export GenBank, GFF3, Fasta • Green boxes are alternative pipeline steps • Dashed boxes are optional pipeline steps 21 July 2016 Phage Genomics - VoM 2016
- 21. In final development: phi-RASTtk FASTA QC FASTA to Genome TO Call rRNAs Call tRNAs Call CDSs Prodigal Call CDSs GenMark Annotate Phage Proteins Annotate Proteins K-mer v2 Find Repeats Find Toxins Export GenBank, GFF3, Fasta • Green boxes are alternative pipeline steps • Dashed boxes are optional pipeline steps 21 July 2016 Phage Genomics - VoM 2016 ✔ ✔ ?
- 22. RASTtk command-line 21 July 2016 Phage Genomics - VoM 2016
- 23. RAST Video demos available • Find & watch: – http://tutorial.theseed.org 21 July 2016 Phage Genomics - VoM 2016
- 24. ACTIVITIES/EXERCISES How to? Phage Genomics - VoM 2016
- 25. What do you need to annotate your genome? • A sequenced genome • Format: fasta or genbank (.gbk) • A RAST username and password • You can find some data to play with at http://egybio.net/tutorial/ 21 July 2016 Phage Genomics - VoM 2016
- 26. 1. Optimize RASTtk for phage 21 July 2016 Phage Genomics - VoM 2016
- 27. 1. Optimize RASTtk for phage 21 July 2016 Phage Genomics - VoM 2016
- 28. 1. Optimize RASTtk for phage 21 July 2016 Phage Genomics - VoM 2016 ✔
- 29. 1. Optimize RASTtk for phage 21 July 2016 Phage Genomics - VoM 2016 ✔
- 30. 1. Optimize RASTtk for phage 21 July 2016 Phage Genomics - VoM 2016
- 31. 1. Optimize RASTtk for phage 21 July 2016 Phage Genomics - VoM 2016 ?
- 32. 1. Optimize RASTtk for phage 21 July 2016 Phage Genomics - VoM 2016 ?
- 33. 1. Optimize RASTtk for phage 21 July 2016 Phage Genomics - VoM 2016
- 34. 1. Optimize RASTtk for phage 21 July 2016 Phage Genomics - VoM 2016
- 35. 1. Optimize RASTtk for phage 21 July 2016 Phage Genomics - VoM 2016
- 36. 2. Command-line RASTtk (Batch option) • Where? – On IRIS (http://tutorial.theseed.org/services/docs/invoc ation/Iris/iris.html) – On your desktop (Download RASTtk) 21 July 2016 Phage Genomics - VoM 2016
- 37. 2. Command-line RASTtk (Batch option) • How? – The key is to convert each contigs file (fasta) to so-called “Genome-typed object” GTO – Once you have GTOs for all your genomes, you can run a couple of commands to annotate each of them OR put them in a folder and annotate in batch 21 July 2016 Phage Genomics - VoM 2016
- 38. 2. Command-line RASTtk (Batch option) • Commands: o rast-create-genome rast-create-genome --scientific-name ”Enterophage Lambda" --genetic-code 11 --domain Virus --contigs lambda.fasta > lambda.gto o rast-process-genome o rast-process-genome-batch o rast-export-genome Details on http://tutorial.theseed.org or follow link from: http://egybio.net/tutorial 21 July 2016 Phage Genomics - VoM 2016
- 39. 2. Command-line RASTtk (Batch option) • If you have 10 extra min, we can try a quick run right after the session (it takes about 10 min to annotate a bacterial genome) 21 July 2016 Phage Genomics - VoM 2016
- 40. 3. Browse your favorite genome 21 July 2016 Phage Genomics - VoM 2016
- 41. 3. Browse your favorite genome 21 July 2016 Phage Genomics - VoM 2016
- 42. 4. Explore the protein page • Annotation history • Annotation clearinghouse • Evidence – similarities – literature 21 July 2016 Phage Genomics - VoM 2016
- 43. 4. Explore the protein page 21 July 2016 Phage Genomics - VoM 2016 • Find your favorite protein
- 44. 4. Explore the protein page 21 July 2016 Phage Genomics - VoM 2016 • Find your favorite protein
- 45. 5. Align proteins (in context) • Evidence> Similarities> Align • Compare region, advanced settings • Phylogenetic trees 21 July 2016 Phage Genomics - VoM 2016
- 46. 5. Align proteins (in context) 21 July 2016 Phage Genomics - VoM 2016
- 47. III. THE COMMUNITY The Opera of PhAnToMe 2.0 21 July 2016 Phage Genomics - VoM 2016
- 48. SEED allows continuous annotation 21 July 2016 SEED RAST GenomesSubsystems SEED Viewer New Genomes Subsystems Editor Phage Genomics - VoM 2016
- 49. SEED allows community annotation 21 July 2016 Phage Genomics - VoM 2016
- 50. Annotations will improve only if YOU help 21 July 2016 Phage Genomics - VoM 2016
- 51. Prospects • Another phage annotation summit? – First summit (Jan 2011) was at Biosphere 2, Tucson, AZ – A second one? • On a summit? (e.g., Bogotá? Mount Sinai?) • Red Sea Resort in Egypt?? • Pushing for community annotation – Undergraduate students (I have about 20 in training) 21 July 2016 Phage Genomics - VoM 2016
- 52. CREDITS The Opera of PhAnToMe 2.0 21 July 2016 Phage Genomics - VoM 2016
- 53. Acknowledgments Robert A. Edwards, PhD • RASTtk and PhiRAST development: Ross Overbeek, Robert Olson, Jim Davis, Gordon Pusch, Terry Disz, Bruce Parrello • Phage annotators (Phantomers): Bhakti Dwivedi, Mya Breitbart, et al. • FIG and all SEED annotators: VeronikaV, SvetaG, OlgaV/Z, et al. 21 July 2016 $$ Phage Genomics - VoM 2016 & NSF Katelyn McNair
- 54. If you use, please cite • SEED, RAST, myRAST, phiRAST, PHAST: – RAST: Aziz et al., BMC Genomics 2008 – SEED servers: Aziz RK,, et al. (2012) PLoS ONE 7(10): e48053. – Nucleic Acids Res. 2014 Jan;42(Database issue):D206-14 21 July 2016 Phage Genomics - VoM 2016