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# Genome annotation with Prokka

<a href="/training-material/hall-of-fame/annasyme/" class="contributor-badge"><img src="https://avatars.githubusercontent.com/annasyme" alt="Avatar">Anna Syme</a> <a href="/training-material/hall-of-fame/tseemann/" class="contributor-badge"><img src="https://avatars.githubusercontent.com/tseemann" alt="Avatar">Torsten Seemann</a> <a href="/training-material/hall-of-fame/slugger70/" class="contributor-badge"><img src="https://avatars.githubusercontent.com/slugger70" alt="Avatar">Simon Gladman</a>

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<div class="footnote" style="bottom: 3em;"><i class="far fa-calendar" aria-hidden="true"></i><span class="visually-hidden">last_modification</span> Updated: Feb 2, 2021</div>
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## Requirements

Before diving into this slide deck, we recommend you to have a look at:

- [Introduction to Galaxy Analyses](/training-material/topics/introduction)

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### <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?

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### <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

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### Overview

- What is genome annotation?

- Tools for genome annotation

- The tool "Prokka"

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- 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.

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### 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".

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### First: assemble the genome
![annotation pic](../../images/contigs.png)

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- 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.

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### Then: annotate
![annotation pic](../../images/seq_annotation.jpg)

???

- 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.

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### Annotation
![annotation pic](../../images/annotation_details.png)

???

- 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.

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### 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.

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### Prokka
![annotation pic](../../images/prokka_pipeline.png)

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- 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.

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### More information
Galaxy Training Network Slides: [Introduction to Genome Annotation](../../slides/introduction.html)

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- More information is available in the "Introduction to Genome Annotation" slides.

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### <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.

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## 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!

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This material is licensed under the <a rel="license" href="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.