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The Opera of Phantome - 2017 (presented at the 22nd Biennial Evergreen Phage Meeting)

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Tools and Methods developed under the SEED/RAST/PhAnToMe (http://www.phantome.org) project and sequels adopted in RASTtk and PATRIC. The tools and database rely on the Subsystems Technology, the SEED (http://theseed.org) environment, and RAST server (http://rast.nmpdr.org).

This is a part of the Phage Genomics Workshop at the 22nd Biennial Evergreen International Phage Meeting, Aug 6 2017.

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The Opera of Phantome - 2017 (presented at the 22nd Biennial Evergreen Phage Meeting)

  1. 1. The Opera of PhAnToMe 2017 Ramy K. Aziz (@azizrk) Aug 6, 2017 opus (LT) = work (Pl. opera) SEED-based phage database (2009-2013-…) Phage Genomics Workshop, Evergreen 2017 giantmicrobes.com
  2. 2. 6 August 2017 History Phage Genomics - Evergreen 2017 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. 3. http://www.phantome.org 6 August 2017 Web portal Phage Genomics - Evergreen 2017
  4. 4. PhAnToMe ToolBox http://www.phantome.org 6 August 2017 Phage Genomics - Evergreen 2017 Very useful
  5. 5. 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 6 August 2017 Phage Genomics - Evergreen 2017
  6. 6. http://rast.nmpdr.org 6 August 2017 Phage Genomics - Evergreen 2017
  7. 7. http://rast.nmpdr.org 6 August 2017 Phage Genomics - Evergreen 2017
  8. 8. “PhAST”: phage-optimized RAST 6 August 2017 Phage Genomics - Evergreen 2017 http://www.phantome.org/PhageSeed/Phage.cgi?page=phast
  9. 9. “PhAST”: phage-optimized RAST 6 August 2017 Phage Genomics - Evergreen 2017 http://www.phantome.org/PhageSeed/Phage.cgi?page=phast
  10. 10. RASTtk (RAST toolkit) 6 August 2017 Phage Genomics - Evergreen 2017
  11. 11. RASTtk command-line 6 August 2017 Phage Genomics - Evergreen 2017
  12. 12. RAST Video demos available • Find & watch: – http://tutorial.theseed.org 6 August 2017 Phage Genomics - Evergreen 2017
  13. 13. PATRIC 6 August 2017 Phage Genomics - Evergreen 2017
  14. 14. PATRIC 6 August 2017 Phage Genomics - Evergreen 2017
  15. 15. PATRIC 6 August 2017 Phage Genomics - Evergreen 2017
  16. 16. DEMO How to? Phage Genomics - Evergreen 2017
  17. 17. 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/ 6 August 2017 Phage Genomics - Evergreen 2017
  18. 18. 1. Optimize RASTtk for phage 6 August 2017 Phage Genomics - Evergreen 2017
  19. 19. 1. Optimize RASTtk for phage 6 August 2017 Phage Genomics - Evergreen 2017
  20. 20. 1. Optimize RASTtk for phage 6 August 2017 Phage Genomics - Evergreen 2017 ✔
  21. 21. 1. Optimize RASTtk for phage 6 August 2017 Phage Genomics - Evergreen 2017 ✔
  22. 22. 1. Optimize RASTtk for phage 6 August 2017 Phage Genomics - Evergreen 2017
  23. 23. 1. Optimize RASTtk for phage 6 August 2017 Phage Genomics - Evergreen 2017 ?
  24. 24. 1. Optimize RASTtk for phage 6 August 2017 Phage Genomics - Evergreen 2017 ?
  25. 25. 1. Optimize RASTtk for phage 6 August 2017 Phage Genomics - Evergreen 2017
  26. 26. 1. Optimize RASTtk for phage 6 August 2017 Phage Genomics - Evergreen 2017 ✔ x
  27. 27. 1. Optimize RASTtk for phage 6 August 2017 Phage Genomics - Evergreen 2017
  28. 28. 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) 6 August 2017 Phage Genomics - Evergreen 2017
  29. 29. 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 6 August 2017 Phage Genomics - Evergreen 2017
  30. 30. 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 6 August 2017 Phage Genomics - Evergreen 2017
  31. 31. 3. Browse your favorite genome 6 August 2017 Phage Genomics - Evergreen 2017
  32. 32. 3. Browse your favorite genome 6 August 2017 Phage Genomics - Evergreen 2017
  33. 33. 4. Explore the protein page • Annotation history • Compare region • Evidence – similarities – literature 6 August 2017 Phage Genomics - Evergreen 2017
  34. 34. 4. Explore the protein page 6 August 2017 Phage Genomics - Evergreen 2017 • Find your favorite protein
  35. 35. 4. Explore the protein page 6 August 2017 Phage Genomics - Evergreen 2017 • Find your favorite protein
  36. 36. 5. Align proteins (in context) • Evidence> Similarities> Align • Compare region, advanced settings • Phylogenetic trees 6 August 2017 Phage Genomics - Evergreen 2017
  37. 37. 5. Align proteins (in context) 6 August 2017 Phage Genomics - Evergreen 2017
  38. 38. THE COMMUNITY The Opera of PhAnToMe 2.0 6 August 2017 Phage Genomics - Evergreen 2017
  39. 39. SEED allows community annotation 6 August 2017 Phage Genomics - Evergreen 2017
  40. 40. Annotations will improve only if YOU help 6 August 2017 Phage Genomics - Evergreen 2017
  41. 41. CREDITS The Opera of PhAnToMe 2.0 6 August 2017 Phage Genomics - Evergreen 2017
  42. 42. 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. 6 August 2017 $$ Phage Genomics - Evergreen 2017 & NSF Katelyn McNair
  43. 43. 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 – PATRIC: Antonopolus et al., Brief. Bioinf. 2017 Jul 31; Online early 6 August 2017 Phage Genomics - Evergreen 2017
  44. 44. Questions?

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