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:

Material

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.

Introduction

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

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to Genome Annotation

Prokaryotes

Annotation of prokaryotic genomes.

Lesson Slides Hands-on Recordings Input dataset Workflows
Bacterial Genome Annotation
Genome annotation with Prokka
Identification of AMR genes in an assembled bacterial genome
Refining Genome Annotations with Apollo (prokaryotes)
Essential genes detection with Transposon insertion sequencing

Eukaryotes

Annotation of eukaryotic genomes.

Lesson Slides Hands-on Recordings Input dataset Workflows
Genome annotation with Helixer
Masking repeats with RepeatMasker
Genome annotation with Funannotate
Genome annotation with Maker (short)
Genome annotation with Maker
Functional annotation of protein sequences
Refining Genome Annotations with Apollo (eukaryotes)
Long non-coding RNAs (lncRNAs) annotation with FEELnc
CRISPR screen analysis

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings Input dataset Workflows
From small to large-scale genome comparison
Comparative gene analysis in unannotated genomes

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:

orcid logoHelena Rasche avatar Helena Rascheorcid logoSimon Gladman avatar Simon Gladmanorcid logoAnthony Bretaudeau avatar Anthony Bretaudeau

Contributors

This material was contributed to by:

orcid logoHelena Rasche avatar Helena Rascheorcid logoErwan Corre avatar Erwan CorreAnton Nekrutenko avatar Anton Nekrutenkoorcid logoAnna Syme avatar Anna SymeNathan Dunn avatar Nathan DunnEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeilorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoPaul Zierep avatar Paul ZierepTorsten Seemann avatar Torsten SeemannTwishi Gulati avatar Twishi Gulatiorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoBérénice Batut avatar Bérénice Batutorcid logoMateo Boudet avatar Mateo BoudetKenji Fujihara avatar Kenji Fujiharaorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoMaria Doyle avatar Maria DoyleBazante Sanders avatar Bazante Sandersorcid logoLaura Leroi avatar Laura Leroiorcid logoBjörn Grüning avatar Björn Grüningorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoSimon Gladman avatar Simon Gladmanorcid logoStéphanie Robin avatar Stéphanie Robin

Funding

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