RODEO (Rapid ORF Description & Evaluation Online) is an algorithm to help biosynthetic gene cluster (BGC) analysis, with an emphasis on ribosomal natural product (RiPP) discovery.
RODEO evaluates one or many genes, characterizing a gene neighborhood based on the presence of profile hidden Markov models (pHMMs). Because RiPP precursor peptides are small and often evade annotation in sequence databases, RODEO can also manually translate small ORFs (open reading frames). A combination of support vector machine (SVM) learning and motif analysis can be used to scan unannotated intergenic regions for RiPP precursors.
With RODEO, thousands of gene clusters can be annotated in a single analysis. We have used RODEO to survey the biosynthetic landscape of certain RiPPs, annotate sequence-similarity networks, annotate phylogenetic trees, decipher evolutionary relationships between enzymes & substrates, and track protein-protein co-occurrence. RODEO works on bacterial, archaeal, and fungal genomes.
NEW! We have just released a new version of RODEO, available for use on the webtool and for download here.
We have a web tool available for simple runs. Feel free to use it! For larger runs or frequent use, consider downloading the program.
We have an installation guide as well as several tutorials.
Manual - requirements, installation & usage
Tutorials (basic) - how to run & customize analyses
Advanced uses - how to use RODEO with other visualization and analysis tools