Genome annotation for prokaryotes
purlPURL: https://gxy.io/GTN:P00003Comment: What is a Learning Pathway?
We recommend you follow the tutorials in the order presented on this page. They have been selected to fit together and build up your knowledge step by step. If a lesson has both slides and a tutorial, we recommend you start with the slides, then proceed with the tutorial.
Learn how to annotate a prokaryotic genome sequence: find the position and function of genes, and even set up a manual curation environment with Apollo.
Module 1: Introduction
General introduction to genome annotation
Time estimation:
Learning Objectives
| Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|
|
Introduction to Genome Annotation
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Module 2: Gene calling and functional annotation
In this module you will learn to run tools to find the position of genes and other genomic components and to functionally annotate them
Time estimation: 3 hours
Learning Objectives
- Run a series of tool to annotate a draft bacterial genome for different types of genomic components
- Evaluate the annotation
- Process the outputs to formate them for visualization needs
- Visualize a draft bacterial genome and its annotations
| Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|
| Bacterial Genome Annotation |
Module 3: Manual curation
Automatic annotation is rarely perfect, in this module you will learn how to start a collaborative manual curation project using Galaxy and Apollo
Time estimation: 3 hours
Learning Objectives
- Load a genome into Galaxy
- View annotations in JBrowse
- Learn how to load JBrowse data into Apollo
- Learn how to manually refine genome annotations within Apollo
- Export refined genome annotations
| Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|
| Refining Genome Annotations with Apollo (prokaryotes) |
Editorial Board
This material is reviewed by our Editorial Board:
Anthony Bretaudeau
Funding
These individuals or organisations provided funding support for the development of this resource
Gallantries
This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.
EuroScienceGateway
EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963.