Creating an Official Gene Set

Overview
Creative Commons License: CC-BY Questions:
  • 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?

Objectives:
  • Validate your genes and create an official gene set from them.

Requirements:
Time estimation: 30 minutes
Supporting Materials:
Published: Nov 2, 2023
Last modification: Nov 1, 2023
License: Tutorial Content is licensed under Creative Commons Attribution 4.0 International License. The GTN Framework is licensed under MIT
purl PURL: https://gxy.io/GTN:T00370
version 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
Agenda

In this tutorial, we will deal with: