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
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14.
PATRIC
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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?