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

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