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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](/archive/2020-12-01/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 Press `C` to create a new window where the same presentation will be displayed. This window is linked to the main window. Changing slides on one will cause the slide to change on the other. Useful when presenting. --- ### <i class="far 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="fas 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="fas 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!
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