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

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

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

http://rast.nmpdr.org

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

RASTtk (RAST toolkit)

RASTtk command-line

RAST Video demos available
• Find & watch:
– http://tutorial.theseed.org

PATRIC

DEMO
How to?

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/

1. Optimize RASTtk for phage

✔

?

✔
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)

• 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

• 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

3. Browse your favorite genome

4. Explore the protein page
• Annotation history
• Compare region
• Evidence
– similarities
– literature

4. Explore the protein page
• Find your favorite protein

5. Align proteins (in context)
• Evidence> Similarities> Align
• Compare region, advanced settings
• Phylogenetic trees

5. Align proteins (in context)

THE COMMUNITY
The Opera of PhAnToMe 2.0

SEED allows community annotation

Annotations will improve
only if YOU help

CREDITS
The Opera of PhAnToMe 2.0

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
$$
&
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

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