1.
PhAnToMe Workshop<br />Phage AnnotationTools and Methods<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

2.
Outline<br />Demonstration:<br />PhAnToMe project<br />PhAnToMe website<br />Phage SEED<br />Vocabulary (PEGs, Subsystems, FIGfams)<br />phiRAST<br />Phage BioBIKE<br />phiSIGNs<br />Tutorial:<br />Browse your favorite genome on SEED<br />Check history and evidence, including similarities<br />Align proteins<br />Explore your phage coverage in metagenomes<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

3.
PhAnToMe Workshop<br />Part IThe Phage SEED Database &The phiRAST Annotation Tool<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

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PhAnToMe: PHageANnotationTOols & MEthods<br />NSF-funded project (2009-2012)<br />Goals:<br />Develop an infrastructure and new tools to generate automated, high-quality annotations of available phage sequences<br />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<br />Engage the insight of the research community to generate an even higher quality of annotation<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

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PhAnToMe: PHageANnotationTOols & MEthods<br />NSF-funded project (2009-2012)<br />Outcomes:<br />PhAnToMe website/portal (http://www.phantome.org)<br />Phage SEED (for already available phage genomes)<br />PhiRAST (for user-uploaded phage genomes)<br />Phage BioBIKE (Graphic programming interface to access phage SEED)<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

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The PhAnToMe website<br />Main features:<br />Tools<br />Downloads<br />PhAnToMers<br />Links & Databases<br />FAQs & News<br />(Labs)<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

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The PhAnToMe website<br />Some highlights:<br />Tools > Phage SEED<br />Tools > Phage Eco-Locator<br />Tools > Phage metadata<br />Tools > PhiSIGNs<br />Community annotation tools<br />Phage SEED > Adopt-a-phage<br />Phage metadata > Phage lifestyle<br />Downloads<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

8.
Phage SEED:Main concepts & vocabulary<br />Protein-based database<br />PEG = protein-encoding gene<br />Functional role ≠ protein name<br />The subsystems approach<br />FIGfams: protein families based on<br />sequence similarity<br />chromosomal co-occurrence<br />human curation<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

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8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />What is a subsystem?<br /> “A subset of functional roles studied across genomes”<br /> A spreadsheet where:<br /> each row represents a genome<br /> each column represents a functional role/ feature/ protein<br /> different patterns = variants<br />

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Advantages of subsystems<br />Subsystems-basedannotation<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

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PhiRAST: automated annotation<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

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What do you need to annotate your genome?<br />A sequenced genome<br />Format: fasta or genbank (.gbk)<br />A RAST username and password<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

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Audience survey<br />Do you have a genome to annotate?<br />Have you uploaded a genome to RAST?<br />What specific requests you have for using SEED, RAST, etc.?<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

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RAST Demo<br />by Karin Holmfeldt<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

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Additional Details<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

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PhAnToMe: PHageANnotationTOols & MEthods<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

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SEED vs. RAST vs. SEED Viewer<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />SEED Viewer<br />RAST<br />New Genomes<br />SEED<br />Subsystems Editor<br />Genomes<br />Subsystems<br />

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What is a FIGfam?<br />Set of proteins that play the same functional role as defined in a column of a curated subsystem and have ≥ 70% similarity<br />Also computed in closely related genomes from conserved sequence and proximity (functional clustering)<br />Cluster-based, computed subsystems of unknown function are offered for exploration and assignment of function for continued improvement of FIGfam annotations<br />Creation of new subsystems or curation of new variants of existing subsystems increases number of functional roles that define FIGfams<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

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PhAnToMe Workshop<br />Part IIPhage BioBIKE<br />by Jeff Elhai et al.<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

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PhAnToMe Workshop<br />Part IIIphiSIGNs<br />by BhaktiDwivedi<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

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PhAnToMe Workshop<br />Part IVHands-on Tutorial<br />Ramy Aziz<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

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I. Browse your favorite genome<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

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II. Explore the protein page<br />Annotation history<br />Annotation clearinghouse<br />Evidence<br />similarities<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

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III. Aligning proteins (in context)<br />Evidence> Similarities> Align<br />Compare region, advanced settings<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />

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IV. Explore your phage vs. metagenomes<br />8/7/11<br />PhAnToMe Workshop-Evergreen 2011<br />