ACT (Artemis Comparison Tool) can disply pairwise comparisons between two or more DNA sequences.
It was alway a pain for me to work with the embl format. Unfortunately for using Artemis and ACT I need embl files again. Tried to install EMBLmyGFF3 with biopython > 1.67 on my laptop.
Retrive the genes (from your query or from the annotation) in a GO term after enrichment.
Simple use of KEGG api for getting references and mapping pathways.
The 8th column of a gff file is critical for extracting protein sequences.
With genome browsers you can view the gene structure but only one at a time. I would like to compare gene models from different methologies and would need a Python/R tool for batch visualisation.
Some self-notes from the book Methods for Computational Gene Prediction by William H. Majoros.
Notes on eukaryotic genome annotation.