name: inverse layout: true class: center, middle, inverse <div class="my-header"><span> <a href="/training-material/topics/genome-annotation" title="Return to topic page" ><i class="fa fa-level-up" aria-hidden="true"></i></a> <a class="nav-link" href="https://github.com/galaxyproject/training-material/edit/main/topics/genome-annotation/tutorials/annotation-with-prokka/slides.html"><i class="fa fa-pencil" aria-hidden="true"></i></a> </span></div> <div class="my-footer"><span> <img src="/training-material/assets/images/GTN-60px.png" alt="Galaxy Training Network" style="height: 40px;"/> </span></div> --- <img src="/training-material/assets/images/GTN.png" alt="Galaxy Training Network" class="cover-logo"/> # Genome annotation with Prokka <div markdown="0"> <div class="contributors-line"> Authors: <a href="/training-material/hall-of-fame/annasyme/" class="contributor-badge contributor-annasyme"><img src="https://avatars.githubusercontent.com/annasyme?s=27" alt="Avatar">Anna Syme</a> <a href="/training-material/hall-of-fame/tseemann/" class="contributor-badge contributor-tseemann"><img src="https://avatars.githubusercontent.com/tseemann?s=27" alt="Avatar">Torsten Seemann</a> <a href="/training-material/hall-of-fame/slugger70/" class="contributor-badge contributor-slugger70"><img src="https://avatars.githubusercontent.com/slugger70?s=27" alt="Avatar">Simon Gladman</a> </div> </div> <div class="footnote" style="bottom: 5.5em;"><i class="far fa-calendar" aria-hidden="true"></i><span class="visually-hidden">last_modification</span> Updated: Feb 2, 2021</div> <div class="footnote" style="bottom: 4em;"><a href="/training-material/videos/watch.html?v=/genome-annotation/tutorials/annotation-with-prokka/slides"><i class="far fa-play-circle" aria-hidden="true"></i><span class="visually-hidden">video-slides</span> View video slides for this lecture</a></div> <div class="footnote" style="bottom: 2.5em;"><i class="fas fa-file-alt" aria-hidden="true"></i><span class="visually-hidden">text-document</span><a href="slides-plain.html"> Plain-text slides</a></div> <div class="footnote" style="bottom: 1em;"><strong>Tip: </strong>press <kbd>P</kbd> to view the presenter notes</div> ??? 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Useful when presenting. --- ## Requirements Before diving into this slide deck, we recommend you to have a look at: - [Introduction to Galaxy Analyses](/training-material/topics/introduction) --- ### <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" ??? - In these slides, we will learn what is genome annotation, and which tools can be used for genome annotation. - We will describe in detail a tool called 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 ??? - Annotating a genome means positioning features along the sequence of a genome. - Those features can be anything one can find in a genome sequence: genes, but also binding sites for example. - When a feature, like a gene for example, is positioned, you can add information about its function. - This operation is named "functional annotation". --- ### First: assemble the genome  ??? - Before annotating a genome, you need to assemble it. - If you get a high quality assembly, it will be easier to perform a good quality annotation. --- ### Then: annotate  ??? - Once you have a good genome sequence, you can annotate it. - In this example, there a gene coding for a delta toxin. - There is a ribosome binding site in red, and the coding sequence of this gene is in green. --- ### Annotation  ??? - For each feature annotated on a genome, you can get its position, its type, and some information about its function or how it is expressed. --- ### 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 ??? - You can annotate features by looking at similarities with known sequences from international databases. - Some tools annotate features on a genome by seeking motifs corresponding to known structure (for example gene or exon start or stop). - Some lab experiments can help annotate specific regions of a genome, even though it is often much more expensive than an automatic annotation. - The lab experiments can provide certainty about function, where automatic annotation is more of a guess. --- ### Prokka  ??? - Prokka is a pipeline that runs several other tools to annotate prokaryotic genomes. - The input is the assembly of the genome in Fasta format. - Prokka runs Aragorn to annotate transfer RNAs. - Ribosomal RNAs are annotated with RNAmmer. - Infernal uses the Rfam database to annotate non coding RNAs. - Finally Prodigal annotated coding genes. - Each coding sequence is then compared to the SwissProt sequence database using Blast, and to TIGR and Pfam motif datases using Hmmer3. - SignalP is also run to detect signal peptides in each predicted coding sequence. - The final result of the whole Prokka pipeline is a set of GFF3, GBK ans ASN1 files. --- ### More information Galaxy Training Network Slides: [Introduction to Genome Annotation](../../slides/introduction.html) ??? - More information is available in the "Introduction to Genome Annotation" slides. --- ### <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://training.galaxyproject.org) and all the contributors! <div markdown="0"> <div class="contributors-line"> Authors: <a href="/training-material/hall-of-fame/annasyme/" class="contributor-badge contributor-annasyme"><img src="https://avatars.githubusercontent.com/annasyme?s=27" alt="Avatar">Anna Syme</a> <a href="/training-material/hall-of-fame/tseemann/" class="contributor-badge contributor-tseemann"><img src="https://avatars.githubusercontent.com/tseemann?s=27" alt="Avatar">Torsten Seemann</a> <a href="/training-material/hall-of-fame/slugger70/" class="contributor-badge contributor-slugger70"><img src="https://avatars.githubusercontent.com/slugger70?s=27" alt="Avatar">Simon Gladman</a> </div> </div> <div style="display: flex;flex-direction: row;align-items: center;justify-content: center;"> <img src="/training-material/assets/images/GTN.png" alt="Galaxy Training Network" style="height: 100px;"/> </div> <a rel="license" href="https://creativecommons.org/licenses/by/4.0/"> This material is licensed under the Creative Commons Attribution 4.0 International License</a>.