How do I perform a genome annotation against my own reference?

Firstly, your reference genome needs to be in a file in GenBank format. You can have multiple GenBank entries in the file (e.g. corresponding to contigs or plasmids). It is crucial that each CDS (coding sequence) feature in the file has a corresponding, unique, locus_tag field in order for gene predictions to be correctly used.

Then, upload your reference genome into xBASE-NG - you will need to register if you haven't already. Ensure that the uploaded file is set to GenBank format.

Then, still logged-in, visit the xBASE Annotation website. You will see an additional drop-down menu where you can choose your supplied reference genome.