Table 2.

List of functions of the SynGenes class in Python

Function name	Function	Parameters
updateSynGenes()	Download SynGenes database from GitHub repository (stable branch)	verbose (bool): Print messages. Default is True
fixGeneName()	Fix Gene Name according to the SynGenes database	geneName (str): Gene name to be fixed type (str): Type of gene (mt = Mitochondrial, cp = Chloroplast). Default is mt verbose (bool): Print messages. Default is True
buildQuery()	Build a query for Entrez search	geneName (str): Gene name to search, must be in the correct format, use the function fixGeneName() to fix the gene name type (str): Type of gene (mt = Mitochondrial, cp = Chloroplast). Default is mt searchType (str): Type of search (Title, Abstract, All Fields, MeSH Terms). Default is All Fields verbose (bool): Print messages. Default is True
buildJson()	Build a JSON file with the data of SynGenes database	fileName (str): Name of the JSON file. Default is SynGenes.js pathSaveFile (str): Path to save the JSON file. Default is SynGenes folder, in the current working directory verbose (bool): Print messages. Default is True
versionSynGenes()	Show the version of SynGenes database	None