Genome Annotation

Overview

Teaching: 10 min
Exercises: 30 min

Questions

• What genes are contained in my genome?

Objectives

• Assigning gene calls to sequence and annotate them with the known databases

Importing and editing Annotation workflow

Import genome annotation workflow:

1. In a new tab, open this link: https://usegalaxy.eu/u/matinnu/w/03annotation
2. On the top-right corner, click the + button (import workflow)
3. Click start using this workflow
4. Click on the name of the newly imported workflow (imported: 03_Annotation) and click Edit
5. Explore the workflow and make changes if necessary

When you are contempt with the workflow, click save. Next, we will run the analysis on the newly assembled genome (sample_02)

1. Click the “play” button on the top-right corner (Run Workflow)
2. If the workflow does not show in detailed view, click Expand to full workflow form
3. Set Send results to a new history to yes.
4. Change the history name to “03_Annotation_2021_sample02”.
5. On the 1: input dataset, select medaka consensus as the input.
6. Click Run Workflow on the top panel.

Prokka: rapid prokaryotic genome annotation

Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.

Discussion 01 - Prokka

1. What kind of output do you get from Prokka?
2. Which outputs can be used for subsequent analysis?

Solution

TBD

Busco:

Busco is a functional quality control based on evolutionarily-informed expectations of gene content of near-universal single-copy orthologs

Discussion 02 - Busco

1. What kind of output do you get from Busco?
2. How do you know if your genome is contaminated or incomplete?
3. What other tools can we use for quality checking our genome completeness and contamination?

Solution

TBD

Key Points

• Genome annotation starts by identifying genes and other functional elements (rRNA, tRNA, etc.) within the nucleotides. This is followed by comparison with databases of interest to predict the functions encoded in the genes.