I have a bed file that containing all Isoseq reads and I would like to remove those overlapped with multiple genes in the annotation file.
Tried several tools to sort gff topologically, incluing genometools, Perl script GFF3sort, Python package tag and pure shell command.
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.