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
Comparison of two annotation tools - Helixer and Braker3
Genome annotation with Braker3
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 logoAnthony Bretaudeau avatar Anthony Bretaudeau

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Contributors

This material was contributed to by:

Nathan Dunn avatar Nathan DunnJasper Ouwerkerk avatar Jasper OuwerkerkGuillaume Gautreau avatar Guillaume Gautreauorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoRomane LIBOUBAN avatar Romane LIBOUBANEsteban Perez-Wohlfeil avatar Esteban Perez-Wohlfeilorcid logoBérénice Batut avatar Bérénice Batutorcid logoMateo Boudet avatar Mateo Boudetorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoLaura Leroi avatar Laura LeroiValentin Loux avatar Valentin Louxorcid logoDeepti Varshney avatar Deepti VarshneyGildas Le Corguillé avatar Gildas Le Corguilléorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoDelphine Lariviere avatar Delphine LariviereKenji Fujihara avatar Kenji FujiharaHélène Chiapello avatar Hélène Chiapelloorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoErwan Corre avatar Erwan Correorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAnika Erxleben avatar Anika ErxlebenEkaterina Polkh avatar Ekaterina Polkhorcid logoHelena Rasche avatar Helena Rascheorcid logoBjörn Grüning avatar Björn Grüningorcid logoSimon Gladman avatar Simon GladmanTwishi Gulati avatar Twishi GulatiWilliam Durand avatar William Durandorcid logoAnna Syme avatar Anna SymeNiall Beard avatar Niall BeardAnton Nekrutenko avatar Anton NekrutenkoBazante Sanders avatar Bazante SandersTorsten Seemann avatar Torsten SeemannSimon Bray avatar Simon Brayorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoTeresa Müller avatar Teresa Müllerorcid logoPaul Zierep avatar Paul Ziereporcid logoMaria Doyle avatar Maria Doyle

Funding

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