Genome Annotation

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.

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Requirements

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

• Introduction to Galaxy Analyses

Material

Introduction

Start here if you are new to genome annotation in Galaxy.

Prokaryotes

Annotation of prokaryotic genomes.

Eukaryotes

Annotation of eukaryotic genomes.

Other

Assorted Tutorials

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

You can also use the following Docker image for these tutorials:

docker run -p 8080:80 quay.io/galaxy/genome-annotation-training

NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.

It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

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Editorial Board

This material is reviewed by our Editorial Board:

Helena Rasche

Simon Gladman

Anthony Bretaudeau

Contributors

This material was contributed to by:

Stéphanie Robin

Jonathan Kreplak

Björn Grüning

Maria Doyle

Twishi Gulati

Anika Erxleben

Nathan Dunn

Kenji Fujihara

Anna Syme

Paul Zierep

Esteban Perez-Wohlfeil

Torsten Seemann

Romane LIBOUBAN

Saskia Hiltemann

Laura Leroi

Bazante Sanders

Mateo Boudet

Erwan Corre

Simon Gladman

Delphine Lariviere

Miaomiao Zhou

Helena Rasche

Alexandre Cormier

Anton Nekrutenko

Avans Hogeschool

Bérénice Batut

Anthony Bretaudeau

Funding

These individuals or organisations provided funding support for the development of this resource

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.

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.

ABRomics