Creating an Official Gene Set
This tutorial is not in its final state. The content may change a lot in the next months. Because of this status, it is also not listed in the topic pages.
I have several genomes assemblies that are not annotated (or I do not trust annotations)
I am interested to compare structure of a particular gene across these genome assemblies
How do I do that?
Validate your genes and create an official gene set from them.Time estimation: 30 minutesSupporting Materials:Published: Nov 2, 2023Last modification: Nov 1, 2023License: Tutorial Content is licensed under Creative Commons Attribution 4.0 International License. The GTN Framework is licensed under MITpurl PURL: https://gxy.io/GTN:T00370version Revision: 2
Here’s how we manage annotations at BIPAA:
- Automatic annotation with Maker
- Apollo server for manual curation, following our guidelines
- Each night, our Apollo report application checks that each annotated gene follows our guidelines. A report is available for each user with a list of errors and warnings that needs to be fixed, and a list of valid gene.
- Regularly we generate a new OGS by merging the automatic annotation with Apollo annotated genes (the valid ones only). We use the ogs_merge script to do that.
- To submit the OGS to ENA @ EBI in EMBL format, we (would like to) use gff2embl
In this tutorial, we will deal with: