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:

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Contributors

This material was contributed to by:

orcid logoErwan Corre avatar Erwan Correorcid logoMaria Doyle avatar Maria Doyleorcid logoHelena Rasche avatar Helena Rascheorcid logoSimon Gladman avatar Simon Gladmanorcid logoLaura Leroi avatar Laura Leroiorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoMiaomiao Zhou avatar Miaomiao ZhouTorsten Seemann avatar Torsten Seemannorcid logoFelicitas Kindel avatar Felicitas KindelNiall Beard avatar Niall BeardEkaterina Polkh avatar Ekaterina Polkhorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoBérénice Batut avatar Bérénice BatutKenji Fujihara avatar Kenji FujiharaEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeilorcid logoBjörn Grüning avatar Björn Grüningorcid logoAnna Syme avatar Anna SymeTeresa Müller avatar Teresa Müllerorcid logoMateo Boudet avatar Mateo Boudetorcid logoJonathan Kreplak avatar Jonathan KreplakSimon Bray avatar Simon BrayAnton Nekrutenko avatar Anton NekrutenkoJasper Ouwerkerk avatar Jasper OuwerkerkBazante Sanders avatar Bazante SandersDeepti Varshney avatar Deepti Varshneyorcid logoAnthony Bretaudeau avatar Anthony BretaudeauWilliam Durand avatar William DurandNathan Dunn avatar Nathan Dunnorcid logoStéphanie Robin avatar Stéphanie RobinGildas Le Corguillé avatar Gildas Le CorguilléTwishi Gulati avatar Twishi Gulatiorcid logoPaul Zierep avatar Paul Zierep

Funding

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