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


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


http://tutorial.theseed.org

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


Questions?

the opera of phantome - 2017 (presented at the 22nd biennial evergreen phage meeting)

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