Genome annotation with Prokka
ContributorsAnna Syme, Torsten Seemann, Simon Gladman
How to annotate a bacterial genome?
How to visualize annoted genomic features?
Load genome into Galaxy
Annotate genome with Prokka
View annotations in JBrowse
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.
- 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.
- 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 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 Slides: Introduction to Genome Annotation
- More information is available in the “Introduction to Genome Annotation” slides.
- Prokka is a useful tool to annotate a bacterial genome.
- JBrowse can be used to inspect the annotation of a genome.