HHMI Logistics Name badges must be worn at all times Restrooms No roaming through the building Questions Ask us Refreshments keep to the schedule Technology Live Streaming The microphones ID: 1036165
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1. SEA-PHAGES Bioinformatics Workshop Overview
2. HHMI Logistics Name badges must be worn at all timesRestroomsNo roaming through the buildingQuestions? – Ask usRefreshments (keep to the schedule)TechnologyLive StreamingThe microphonesClickShare
3. Characterize and investigate phage genomes including the details of gene calling, functional assignments, and preparing final submission files that meet QC requirements. This year’s genome is mycobacteriophage RagingRooster. Install and use the software for annotation and analysis of phages. The software includes DNA Master, Phamerator, and other web-based tools. Identify basic phage biology concepts that underlie bioinformatic investigations.Explore classroom implementation strategies.Objectives
4. Primary Learning MethodLearn by doingGather dataDo the work: annotate & analyze the genomeDo science like scientists do it. [Translation: new technology changes at a moment’s notice]
5. Workshop LogisticsWorkshop page at seaphages.orgWe will be working in groups (assignments are on Workshop page) Introducing a revised and expanded SEA-PHAGES Bioinformatics GuideLab notebook. Take notes while annotating!seaphages.org forums: Let’s model that at the workshop so it will be easy later!
6. We Will…Use RagingRooster’s genome toLearn to manipulate the tools we useDNA MasterGeneMark, GlimmerBLASTPhameratorHHpredStarteratorPractice calling genes and functionsInvestigate other types of genes you will come across Produce a quality genome annotationSequence quality control: ✓Annotation quality control: Checklist and files
7. Biological Information FlowSequencing and Finishing GenomesBionformatic Information FlowImportant Context
8. Phage discovery and isolationDNA sequencing/assembly/QCIn-class annotationFinal annotation filesAnnotation QC (SMART)GenBank submissionPhage DNA and lysates
9. Phage discovery and isolationPhage DNA and lysatesDNA sequencing/assembly/QCIn-class annotationFinal annotation filesAnnotation QC (SMART)GenBank submission
10. Phage discovery and isolationPhage DNA and lysatesDNA sequencing/assembly/QCIn-class annotationFinal annotation filesAnnotation QC (SMART)GenBank submissionAuto annotate in DNA MasterManually improve annotationCall functionsPrepare final filesPreliminary genome investigation
11. Phage discovery and isolationPhage DNA and lysatesDNA sequencing/assembly/QCIn-class annotationFinal annotation filesAnnotation QC (SMART)GenBank submissionAuto annotate in DNA MasterManually improve annotationCall functionsPrepare final filesPreliminary genome investigationBLASTn genomeGenerate GeneMark outputMake Phamerator mapAdd/delete genesImprove start sitesCalls tRNAs, frameshifts, …Merge annotationsFinalize and perfect notes