Introduction to PhAnToMe Workshop, 19th Evergreen Phage Meeting, 2011

PhAnToMe Workshop
Phage AnnotationTools and Methods
8/7/11
PhAnToMe Workshop-Evergreen 2011

Outline
Demonstration:
PhAnToMe project
PhAnToMe website
Phage SEED
Vocabulary (PEGs, Subsystems, FIGfams)
phiRAST
Phage BioBIKE
phiSIGNs
Tutorial:
Browse your favorite genome on SEED
Check history and evidence, including similarities
Align proteins
Explore your phage coverage in metagenomes
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PhAnToMe Workshop
Part IThe Phage SEED Database &The phiRAST Annotation Tool
8/7/11

PhAnToMe: PHageANnotationTOols & MEthods
NSF-funded project (2009-2012)
Goals:
Develop an infrastructure and new tools to generate automated, high-quality annotations of available phage sequences
Develop a resource through which the annotation and tools are made available to those who study phages in such a way that they can use them creatively
Engage the insight of the research community to generate an even higher quality of annotation
8/7/11

NSF-funded project (2009-2012)
Outcomes:
PhAnToMe website/portal (http://www.phantome.org)
Phage SEED (for already available phage genomes)
PhiRAST (for user-uploaded phage genomes)
Phage BioBIKE (Graphic programming interface to access phage SEED)
8/7/11

The PhAnToMe website
Main features:
Tools
Downloads
PhAnToMers
Links & Databases
FAQs & News
(Labs)
8/7/11

The PhAnToMe website
Some highlights:
Tools > Phage SEED
Tools > Phage Eco-Locator
Tools > Phage metadata
Tools > PhiSIGNs
Community annotation tools
Phage SEED > Adopt-a-phage
Phage metadata > Phage lifestyle
Downloads
8/7/11

Phage SEED:Main concepts & vocabulary
Protein-based database
PEG = protein-encoding gene
Functional role ≠ protein name
The subsystems approach
FIGfams: protein families based on
sequence similarity
chromosomal co-occurrence
human curation
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8/7/11
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

Advantages of subsystems
Subsystems-basedannotation
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PhiRAST: automated annotation
8/7/11

What do you need to annotate your genome?
A sequenced genome
Format: fasta or genbank (.gbk)
A RAST username and password
8/7/11

Audience survey
Do you have a genome to annotate?
Have you uploaded a genome to RAST?
What specific requests you have for using SEED, RAST, etc.?
8/7/11

RAST Demo
by Karin Holmfeldt
8/7/11

Additional Details
8/7/11

8/7/11

SEED vs. RAST vs. SEED Viewer
8/7/11
SEED Viewer
RAST
New Genomes
SEED
Subsystems Editor
Genomes
Subsystems

What is a FIGfam?
Set of proteins that play the same functional role as defined in a column of a curated subsystem and have ≥ 70% similarity
Also computed in closely related genomes from conserved sequence and proximity (functional clustering)
Cluster-based, computed subsystems of unknown function are offered for exploration and assignment of function for continued improvement of FIGfam annotations
Creation of new subsystems or curation of new variants of existing subsystems increases number of functional roles that define FIGfams
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PhAnToMe Workshop
Part IIPhage BioBIKE
by Jeff Elhai et al.
8/7/11

PhAnToMe Workshop
Part IIIphiSIGNs
by BhaktiDwivedi
8/7/11

PhAnToMe Workshop
Part IVHands-on Tutorial
Ramy Aziz
8/7/11

I. Browse your favorite genome
8/7/11

II. Explore the protein page
Annotation history
Annotation clearinghouse
Evidence
similarities
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III. Aligning proteins (in context)
Evidence> Similarities> Align
Compare region, advanced settings
8/7/11

IV. Explore your phage vs. metagenomes
8/7/11

Introduction to PhAnToMe Workshop, 19th Evergreen Phage Meeting, 2011

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Introduction to PhAnToMe Workshop, 19th Evergreen Phage Meeting, 2011 Presentation Transcript