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--- # Genome annotation with Prokka --- ## Requirements Before diving into this slide deck, we recommend you to have a look at: - [Introduction to Galaxy Analyses](/training-material/topics/introduction) .footnote[Tip: press `P` to view the presenter notes] ??? Presenter notes contain extra information which might be useful if you intend to use these slides for teaching. Press `P` again to switch presenter notes off --- ### <i class="fa fa-question-circle" aria-hidden="true"></i><span class="visually-hidden">question</span> Questions - How to annotate a bacterial genome? - How to visualize annoted genomic features? --- ### <i class="fa fa-bullseye" aria-hidden="true"></i><span class="visually-hidden">objectives</span> Objectives - Load genome into Galaxy - Annotate genome with Prokka - View annotations in JBrowse --- <!-- To show speaker notes during a presentation: press c to clone the slides (opens a new window) on one window, press p to show speaker notes display the other window --> ### Overview - What is genome annotation? - Tools for genome annotation - The tool "Prokka" --- ### What is Annotation? - Classifying and describing parts of the genome sequence - Annotations are biological or other features on a genome, *e.g.* - a ribosome binding site: a biological feature - a sequence of TTTTTT: may/may not be biological but could be interesting - We can name features by type and location, *e.g.* gene, pseudogene, repeat - We can hypothesise functions, *e.g.* antioxidant activity --- ### First: assemble the genome ![annotation pic](../../images/contigs.png) --- ### Then: annotate ![annotation pic](../../images/seq_annotation.jpg) --- ### Annotation ![annotation pic](../../images/annotation_details.png) --- ### How do we annotate? many different ways: - sequence: does it match known sequences in databases? - sequence structure: *e.g.* does it look like an exon (start and stop codons)? - use other data: *e.g.* do lab experiments to investigate biological function --- ### Prokka ![annotation pic](../../images/prokka_pipeline.png) --- ### More information Galaxy Training Network Slides: Introduction to Genome Annotation --- ### <i class="fa fa-key" aria-hidden="true"></i><span class="visually-hidden">keypoints</span> Key points - Prokka is a useful tool to annotate a bacterial genome. - JBrowse can be used to inspect the annotation of a genome. --- ## Thank you! This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://wiki.galaxyproject.org/Teach/GTN) and all the contributors!