RODEO

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 diagram

Command-line update notice

12/10/2018: Command-line users experiencing HTTP 429 errors are encouraged to update RODEO from our GitHub.

Introduction

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.

Web Tool

We have a web tool available for simple runs. Feel free to use it! For larger runs or frequent use, consider downloading the program.

Documentation

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

Download

The latest version of the RODEO source code, as well as supporting scripts, can be downloaded from our GitHub or obtained by contacting the Mitchell lab.

RODEO is powered by HMMER, Biopython, GenBank, Pfam, TIGRFAM, MEME, and scikit-learn.

Get RODEO»