HMM reference database for prediction of O-antigen serogroup in V. cholerae genomes

To predict the antigenic serogroup, we screened the assemblies against a custom reference database using Hamburger (Williams, 2021). Details of reference sequences and loci are supplied in the 'serogrouping_reference_sequence.xlsx' spreadsheet. In brief, a database was constructed by selecting flanking and marker genes for the operon encoding the <em>V. cholerae</em> O-antigen, with representative genes for both O1 and non-O1 serogroups included. Gene sequences were individually aligned using Clustal Omega (version 1.2.4), prior to HMM construction with HMMER (version 3.2.1) and concatenation of the HMM alignments. Assemblies were screened against this database using Hamburger (version 836a77c) to identify the operon, and genetic structure was compared across the assemblies and references to designate serogroups.