Gene Annotation
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This course introduces annotation, such as structural gene annotation with EGNEP or MAKER workflows, in the Plant Genomme Assembly and Annotation course, both in a theoretical and practical way, with hands-on practice sessions. It will help you to configure and run your own pipelines using these tools through command-line interface. |
MAKER2 : An annotation pipeline and genome-database management tool for second-generation genome projects. Holt, Carson; Yandell, Mark. BMC Bioinformatics, Vol. 12, No. 1, 491, 22.12.2011. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-491.
Genome Annotation in Plants and Fungi: EuGène as a Model Platform. Sylvain Foissac et al. Current Bioinformatics, 2008. DOI: 10.2174/157489308784340702
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data.
Carver T, Harris SR, Berriman M, Parkhill J and McQuillan JA. Bioinformatics (Oxford, England) 2012;28;4;464-9
PMID:22199388
Prerequisites
Prior knowledge on workflow execution not necessary
Basic knowledge of Linux (Linux for dummies required)
Program
- Why using a combiner / integrator to annotate gene ?
- How to annotate a eukaryotic genome ?
- How to configure / to customize gene annotation workflow ?
- How to execute them?
- Use case
Learning objectives
- Have revised the structure of an eukaryotic gene.
- Learned what is annotation of eukaryotic genes.
- Understood the major steps of a combiner like EuGene.
- Explaining the major steps of MAKER and EuGène,
in which way they differ from each other. - Annotating your genome with MAKER and EuGène.
- Know how to Launch a virtual machine on IFB cloud.
- Know how to configure and run MAKER VM / Eugene VM on the Arabidopsis genome.
- Know how to Assess the results with Busco.
Training material
Instructors
- Jacques Dainat (JD) - jacques.dainat@nbis.se
- Lucile Soler (LS) - lucile.soler@nbis.se
- Stéphanie Bocs (SSB) - stephanie.sidibe-bocs@cirad.fr
- Laurent Bouri (LB) - Laurent.BOURI@france-bioinformatique.fr
- Jonathan Lorenzo (JL) - jonathan.lorenzo@france-bioinformatique.fr
Trainings
| Date | Location | Topics | Participants | Instructors | Links | Units |
|---|---|---|---|---|---|---|
| 2018 | Montpellier, France | PGAA | 22 | JD, LS, SB, LB, JL | Elixir GAA wiki PGAA course announcement Elixir e-learning platform | IRD, Cirad, Montpellier SupAgro, INRA, IPS2, Neiker, RWTH Aachen University |
