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 logoSimon Gladman avatar Simon Gladmanorcid logoFelicitas Kindel avatar Felicitas Kindelorcid logoErwan Corre avatar Erwan CorreSimon Bray avatar Simon Brayorcid logoLaura Leroi avatar Laura LeroiNathan Dunn avatar Nathan DunnBazante Sanders avatar Bazante Sandersorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoJonathan Kreplak avatar Jonathan Kreplakorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoAlexandre Cormier avatar Alexandre CormierTeresa Müller avatar Teresa MüllerEsteban Perez-Wohlfeil avatar Esteban Perez-WohlfeilNiall Beard avatar Niall Beardorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoMaria Doyle avatar Maria Doyleorcid logoMateo Boudet avatar Mateo Boudetorcid logoCristóbal Gallardo avatar Cristóbal GallardoJasper Ouwerkerk avatar Jasper Ouwerkerkorcid logoStéphanie Robin avatar Stéphanie RobinAnton Nekrutenko avatar Anton Nekrutenkoorcid logoAnna Syme avatar Anna SymeGildas Le Corguillé avatar Gildas Le Corguilléorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoNicola Soranzo avatar Nicola SoranzoTwishi Gulati avatar Twishi GulatiTorsten Seemann avatar Torsten SeemannWilliam Durand avatar William DurandEkaterina Polkh avatar Ekaterina Polkhorcid logoHelena Rasche avatar Helena Rascheorcid logoBjörn Grüning avatar Björn GrüningKenji Fujihara avatar Kenji Fujiharaorcid logoPaul Zierep avatar Paul Ziereporcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoBérénice Batut avatar Bérénice Batutorcid logoSaskia Hiltemann avatar Saskia HiltemannDeepti Varshney avatar Deepti Varshney

Funding

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