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Galaxy Training Network



Genome annotation with Prokka



Updated:   PURL: gxy.io/GTN:S00065

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Galaxy Training Network

Requirements

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

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Galaxy Training Network

Questions

  • How to annotate a bacterial genome?

  • How to visualize annoted genomic features?

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Objectives

  • Load genome into Galaxy

  • Annotate genome with Prokka

  • View annotations in JBrowse

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Galaxy Training Network

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.
Galaxy Training Network

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

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  • 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".
Galaxy Training Network

First: assemble the genome

annotation pic

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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.
Galaxy Training Network

Then: annotate

annotation pic

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  • 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.
Galaxy Training Network

Annotation

annotation pic

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  • 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.
Galaxy Training Network

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

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  • 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.
Galaxy Training Network

Prokka

annotation pic

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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.

Galaxy Training Network

More information

Galaxy Training Network Slides: Introduction to Genome Annotation

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

Galaxy Training Network

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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Galaxy Training Network

Thank You!

This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors!

Galaxy Training Network

Tutorial Content is licensed under Creative Commons Attribution 4.0 International License.

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Galaxy Training Network

Requirements

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

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