Rapid tutorial of how to use RAST for phage annotation, presented at The 2018 EMBO Viruses of Microbes (VoM) meeting in Wroclaw, Poland

3. What will be covered?
1. Annotation overview
2. Using the RAST family for genome annotation:
– Optimizing RAST for phages
– Command line/ Batch options
3. Introducing PATRIC and resources in
development
– Therapeutic phage database
– Assembly
– Variation analysis
– Metagenome binning
9 July 2018 Phage Genomics - VoM 2018

4. Subsystems-based tools & SEED
http://theseed.org
9 July 2018
Aziz RK,, et al. (2012) PLoS ONE 7(10): e48053. doi:10.1371/journal.pone.0048053
Phage Genomics - VoM 2018

5. SEED Subsystems: Main concept
One genome
All genomes
9 July 2018 Phage Genomics - VoM 2018

6. SEED Subsystems: Main concept
One genome
All genomes
9 July 2018 Phage Genomics - VoM 2018
“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”

7. 9 July 2018
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 2018

8. RAST (http://rast.nmpdr.org)
9 July 2018 Phage Genomics - VoM 2018

9. RAST: automated annotation
9 July 2018 Phage Genomics - VoM 2018

10. Subsystems-based tools
(Extended RAST family)
• (At least) Five ways to annotate a genome via RAST:
– RAST (http://rast.nmpdr.org)
• annotates online, saves your genome on server
– Use your favorite gene caller then upload gbk file to RAST
– myRAST (local)
• uses the server but you can edit offline)
– RASTtk (second-generation RAST)
• modular
• batch upload
– PATRIC
– Coming Soon: new gene caller Phanotator
9 July 2018 Phage Genomics - VoM 2018

11. http://rast.nmpdr.org
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12. http://rast.nmpdr.org
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13. RASTtk (RAST toolkit)
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14. RASTtk command-line
9 July 2018 Phage Genomics - VoM 2018

15. RAST Video demos available
• Find & watch:
– http://tutorial.theseed.org
9 July 2018 Phage Genomics - VoM 2018

16. TUTORIAL 1: USING RAST
FOR PHAGE ANNOTATION
How to?
Phage Genomics - VoM 20189 July 2018

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 test data (T4, T7,
Lambda) at http://egybio.net/tutorial
9 July 2018 Phage Genomics - VoM 2018

18. 1. Optimizing RASTtk for phage
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19. 1. Optimizing RASTtk for phage
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20. 1. Optimizing RASTtk for phage
9 July 2018 Phage Genomics - VoM 2018
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21. 1. Optimizing RASTtk for phage
9 July 2018 Phage Genomics - VoM 2018
✔

22. 1. Optimizing RASTtk for phage
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23. 1. Optimizing RASTtk for phage
9 July 2018 Phage Genomics - VoM 2018
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24. 1. Optimizing RASTtk for phage
9 July 2018 Phage Genomics - VoM 2018
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25. 1. Optimizing RASTtk for phage
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26. 1. Optimizing RASTtk for phage
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27. 1. Optimizing RASTtk for phage
9 July 2018 Phage Genomics - VoM 2018

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)
9 July 2018 Phage Genomics - VoM 2018

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
9 July 2018 Phage Genomics - VoM 2018

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
9 July 2018 Phage Genomics - VoM 2018

31. Next  PATRIC (patricbrc.org)
9 July 2018 Phage Genomics - VoM 2018

32. COMMUNITY STANDARDS,
METADATA AND ANNOTATIONS
Subsystems-based tools
9 July 2018 Phage Genomics - VoM 2018

33. SEED allows continuous annotation
9 July 2018
SEED
RAST
GenomesSubsystems
SEED Viewer
New Genomes
Subsystems
Editor
Phage Genomics - VoM 2018

34. SEED allows community annotation
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35. Annotations will improve
only if YOU help
9 July 2018 Phage Genomics - VoM 2018