RRE-Finder

A Genome-Mining Tool for Class-Independent RiPP Discovery. Bioinformatic application for the detection of RREs in protein sequences of interest. Install the included conda environment with "conda env create -f RREfinder.yml" Or make sure the following packages/programs are installed and in your path. Databases need to be downloaded independently from https://zenodo.org/record/3733240#.XoRkIUEzbCI. Please download all the files, except the folder with the seed sequences, and place them into the data/database folder within the downloaded repository. RREFinder accepts both protein .fasta files and .genbank files. Alternatively, you can use '--antismash ripp' and let the --infile point to a .final.gbk file from antiSMASH analysis. This way all the antiSMASH RiPP gene clusters will be analyzed.