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

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An introduction to a tutorial on using the PhAnToMe (Phage Annotation Tools and Methods) website, databases (Phage SEED, Phage Metadata), and programs: phiRAST, PhageBioBIKE, and phiSIGNs

An introduction to a tutorial on using the PhAnToMe (Phage Annotation Tools and Methods) website, databases (Phage SEED, Phage Metadata), and programs: phiRAST, PhageBioBIKE, and phiSIGNs

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

  • 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
    8/7/11
    PhAnToMe Workshop-Evergreen 2011
  • PhAnToMe Workshop
    Part IThe Phage SEED Database &The phiRAST Annotation Tool
    8/7/11
    PhAnToMe Workshop-Evergreen 2011
  • 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
    PhAnToMe Workshop-Evergreen 2011
  • PhAnToMe: PHageANnotationTOols & MEthods
    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
    PhAnToMe Workshop-Evergreen 2011
  • The PhAnToMe website
    Main features:
    Tools
    Downloads
    PhAnToMers
    Links & Databases
    FAQs & News
    (Labs)
    8/7/11
    PhAnToMe Workshop-Evergreen 2011
  • 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
    PhAnToMe Workshop-Evergreen 2011
  • 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
    8/7/11
    PhAnToMe Workshop-Evergreen 2011
  • 8/7/11
    PhAnToMe Workshop-Evergreen 2011
    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
    8/7/11
    PhAnToMe Workshop-Evergreen 2011
  • PhiRAST: automated annotation
    8/7/11
    PhAnToMe Workshop-Evergreen 2011
  • What do you need to annotate your genome?
    A sequenced genome
    Format: fasta or genbank (.gbk)
    A RAST username and password
    8/7/11
    PhAnToMe Workshop-Evergreen 2011
  • 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
    PhAnToMe Workshop-Evergreen 2011
  • RAST Demo
    by Karin Holmfeldt
    8/7/11
    PhAnToMe Workshop-Evergreen 2011
  • Additional Details
    8/7/11
    PhAnToMe Workshop-Evergreen 2011
  • PhAnToMe: PHageANnotationTOols & MEthods
    8/7/11
    PhAnToMe Workshop-Evergreen 2011
  • SEED vs. RAST vs. SEED Viewer
    8/7/11
    PhAnToMe Workshop-Evergreen 2011
    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
    8/7/11
    PhAnToMe Workshop-Evergreen 2011
  • PhAnToMe Workshop
    Part IIPhage BioBIKE
    by Jeff Elhai et al.
    8/7/11
    PhAnToMe Workshop-Evergreen 2011
  • PhAnToMe Workshop
    Part IIIphiSIGNs
    by BhaktiDwivedi
    8/7/11
    PhAnToMe Workshop-Evergreen 2011
  • PhAnToMe Workshop
    Part IVHands-on Tutorial
    Ramy Aziz
    8/7/11
    PhAnToMe Workshop-Evergreen 2011
  • I. Browse your favorite genome
    8/7/11
    PhAnToMe Workshop-Evergreen 2011
  • II. Explore the protein page
    Annotation history
    Annotation clearinghouse
    Evidence
    similarities
    8/7/11
    PhAnToMe Workshop-Evergreen 2011
  • III. Aligning proteins (in context)
    Evidence> Similarities> Align
    Compare region, advanced settings
    8/7/11
    PhAnToMe Workshop-Evergreen 2011
  • IV. Explore your phage vs. metagenomes
    8/7/11
    PhAnToMe Workshop-Evergreen 2011