Notebook for Processing GTDB Reference Proteomes to find Hmf Homologues
Abstract
Python notebook to accompany paper submission "Design, characterization and application of a biosensor for 2,5-furandicarboxylic acid" by Bhumishree Bhumisuta Dehury, Lani Peel, Thomas Butterfield, Karl A. P. Payne, Mary Ortmayer, Colin Levy, David Leys and Neil Dixon. Code sanitises input GTDB reference proteomes to allow searching for homologues to the Cupriavidus basilensis Hmf operon proteins using DIAMOND. Code then parses DIAMOND hits file, processes the data and outputs CSV tables that were used to generate the figures in the paper.
Fields of Study & Subjects
Genomics and Phylogenetic Studies
Microbial Metabolic Engineering and Bioproduction
Bacterial Genetics and Biotechnology
Publication details
- Journal / source
- Zenodo (CERN European Organization for Nuclear Research)
- Publication date
- 29 January 2026
- Document type
- Book