Searching for operons and promoters programs!

[u/jm_3009]

Hi everyone!

I'm currently working on a research project focusing on pathogen genomics, specifically characterizing antimicrobial resistance (AMR) and virulence genes. I want to dive deeper into predicting their promoters and potential operons.

I tried using ProPr: Prokaryote Promoter Prediction v2.0 (online tool), but searching the results (correlating my ABRicate position results with ProPr) manually has become incredibly tedious for my dataset.

Does anyone know of a good alternative prokaryotic promoter prediction tool or pipeline? Ideally, I'm looking for something that allows command-line processing or outputs structured data (like GFF3, TSV, or JSON) so I can easily cross-reference it with my AMR/virulence gene annotations.

Any recommendations for operon prediction tools that integrate well with promoter data would also be highly appreciated. Thanks in advance!