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

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This document provides an overview of the PhAnToMe database and annotation tools for phage genomics. It discusses the history and development of PhAnToMe, an NSF-funded project involving multiple research centers. It describes the PhAnToMe toolbox and annotation tools like RAST, PhAST, myRAST, RASTtk, and PATRIC. Steps are outlined for optimizing RASTtk for phage, using command-line RASTtk, browsing genomes, exploring protein pages, aligning proteins, and acknowledging the community contributions that improve annotations.

Science

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

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

http://www.phantome.org
6 August 2017
Web portal
Phage Genomics - Evergreen 2017

PhAnToMe ToolBox
http://www.phantome.org
6 August 2017 Phage Genomics - Evergreen 2017
Very useful

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

http://rast.nmpdr.org
6 August 2017 Phage Genomics - Evergreen 2017

“PhAST”: phage-optimized RAST
6 August 2017 Phage Genomics - Evergreen 2017
http://www.phantome.org/PhageSeed/Phage.cgi?page=phast

RASTtk (RAST toolkit)
6 August 2017 Phage Genomics - Evergreen 2017

RASTtk command-line
6 August 2017 Phage Genomics - Evergreen 2017

RAST Video demos available
• Find & watch:
– http://tutorial.theseed.org
6 August 2017 Phage Genomics - Evergreen 2017

PATRIC
6 August 2017 Phage Genomics - Evergreen 2017

DEMO
How to?
Phage Genomics - Evergreen 2017

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

1. Optimize RASTtk for phage
6 August 2017 Phage Genomics - Evergreen 2017

1. Optimize RASTtk for phage
6 August 2017 Phage Genomics - Evergreen 2017
✔
x

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

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

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

3. Browse your favorite genome
6 August 2017 Phage Genomics - Evergreen 2017

4. Explore the protein page
• Annotation history
• Compare region
• Evidence
– similarities
– literature
6 August 2017 Phage Genomics - Evergreen 2017

4. Explore the protein page
6 August 2017 Phage Genomics - Evergreen 2017
• Find your favorite protein

5. Align proteins (in context)
• Evidence> Similarities> Align
• Compare region, advanced settings
• Phylogenetic trees
6 August 2017 Phage Genomics - Evergreen 2017

5. Align proteins (in context)
6 August 2017 Phage Genomics - Evergreen 2017

THE COMMUNITY
The Opera of PhAnToMe 2.0
6 August 2017 Phage Genomics - Evergreen 2017

SEED allows community annotation
6 August 2017 Phage Genomics - Evergreen 2017

Annotations will improve
only if YOU help
6 August 2017 Phage Genomics - Evergreen 2017

CREDITS
The Opera of PhAnToMe 2.0
6 August 2017 Phage Genomics - Evergreen 2017

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

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

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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 - 2017 (presented at the 22nd Biennial Evergreen Phage Meeting)

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. 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. http://www.phantome.org 6 August 2017 Web portal Phage Genomics - Evergreen 2017

4. PhAnToMe ToolBox http://www.phantome.org 6 August 2017 Phage Genomics - Evergreen 2017 Very useful

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. http://rast.nmpdr.org 6 August 2017 Phage Genomics - Evergreen 2017

7. http://rast.nmpdr.org 6 August 2017 Phage Genomics - Evergreen 2017

8. “PhAST”: phage-optimized RAST 6 August 2017 Phage Genomics - Evergreen 2017 http://www.phantome.org/PhageSeed/Phage.cgi?page=phast

9. “PhAST”: phage-optimized RAST 6 August 2017 Phage Genomics - Evergreen 2017 http://www.phantome.org/PhageSeed/Phage.cgi?page=phast

10. RASTtk (RAST toolkit) 6 August 2017 Phage Genomics - Evergreen 2017

11. RASTtk command-line 6 August 2017 Phage Genomics - Evergreen 2017

12. RAST Video demos available • Find & watch: – http://tutorial.theseed.org 6 August 2017 Phage Genomics - Evergreen 2017

13. PATRIC 6 August 2017 Phage Genomics - Evergreen 2017

14. PATRIC 6 August 2017 Phage Genomics - Evergreen 2017

15. PATRIC 6 August 2017 Phage Genomics - Evergreen 2017

16. DEMO How to? Phage Genomics - Evergreen 2017

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. 1. Optimize RASTtk for phage 6 August 2017 Phage Genomics - Evergreen 2017

19. 1. Optimize RASTtk for phage 6 August 2017 Phage Genomics - Evergreen 2017

20. 1. Optimize RASTtk for phage 6 August 2017 Phage Genomics - Evergreen 2017 ✔

21. 1. Optimize RASTtk for phage 6 August 2017 Phage Genomics - Evergreen 2017 ✔

22. 1. Optimize RASTtk for phage 6 August 2017 Phage Genomics - Evergreen 2017

23. 1. Optimize RASTtk for phage 6 August 2017 Phage Genomics - Evergreen 2017 ?

24. 1. Optimize RASTtk for phage 6 August 2017 Phage Genomics - Evergreen 2017 ?

25. 1. Optimize RASTtk for phage 6 August 2017 Phage Genomics - Evergreen 2017

26. 1. Optimize RASTtk for phage 6 August 2017 Phage Genomics - Evergreen 2017 ✔ x

27. 1. Optimize RASTtk for phage 6 August 2017 Phage Genomics - Evergreen 2017

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. 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. 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. 3. Browse your favorite genome 6 August 2017 Phage Genomics - Evergreen 2017

32. 3. Browse your favorite genome 6 August 2017 Phage Genomics - Evergreen 2017

33. 4. Explore the protein page • Annotation history • Compare region • Evidence – similarities – literature 6 August 2017 Phage Genomics - Evergreen 2017

34. 4. Explore the protein page 6 August 2017 Phage Genomics - Evergreen 2017 • Find your favorite protein

35. 4. Explore the protein page 6 August 2017 Phage Genomics - Evergreen 2017 • Find your favorite protein

36. 5. Align proteins (in context) • Evidence> Similarities> Align • Compare region, advanced settings • Phylogenetic trees 6 August 2017 Phage Genomics - Evergreen 2017

37. 5. Align proteins (in context) 6 August 2017 Phage Genomics - Evergreen 2017

38. THE COMMUNITY The Opera of PhAnToMe 2.0 6 August 2017 Phage Genomics - Evergreen 2017

39. SEED allows community annotation 6 August 2017 Phage Genomics - Evergreen 2017

40. Annotations will improve only if YOU help 6 August 2017 Phage Genomics - Evergreen 2017

41. CREDITS The Opera of PhAnToMe 2.0 6 August 2017 Phage Genomics - Evergreen 2017

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. 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. Questions?

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

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