Nelly Sélem edited this page Feb 14, 2018 · 39 revisions

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EvoMining

EvoMining is a functional phylogenomics method for identification of expanded, repurposed enzyme families, with the potential to catalyze new conversions in natural product biosynthesis. EvoMining software is a standalone tool distributed as a docker image developed by the Evolution of metabolic diversity lab (EvoDivMet). EvoMining docker image has been tested on Ubuntu 14 and Mac OS 10.13.1.

Usage

Please consult Installation guide, Example and sample data and Tutorial

Introduction

Given an enzyme family EvoMining helps to identify recruitments of family expansions, into natural products biosynthetic gene clusters (BGCs) within the scope of a custom genomic database. EvoMining is a visual, evolutionary based genome mining tool with the milestone of prioritize non standard secondary metabolite biosynthetic pathways. The algorithm follows enzyme families from central pathways on their recruitment as components of natural products (NPs) biosynthetic gene clusters (BGCs). EvoMining assumption is that enzyme families are expanded frequently either by duplication or by horizontal gene transfer on prokaryotic genomes. These additional gene copies represents evolutionary raw material with high potential to be recruited into secondary metabolism to perform novel chemical functionalities.

EvoMining allows identification of potentially divergent sequences from an expanded enzyme family, evominig-hits can be processed by CORASON to identify variation on its cluster, so on perspective EvoMining and CORASON together can help to prioritize clusters that may be involved on chemical novelty.

EvoMining citation

Cruz-Morales, Pablo, Johannes Florian Kopp, Christian Martínez-Guerrero, Luis Alfonso Yáñez-Guerra, Nelly Selem-Mojica, Hilda Ramos-Aboites, Jörg Feldmann, and Francisco Barona-Gómez. 2016. “Phylogenomic Analysis of Natural Products Biosynthetic Gene Clusters Allows Discovery of Arseno-Organic Metabolites in Model Streptomycetes.” Genome Biology and Evolution 8 (6): 1906–16. doi:10.1093/gbe/evw125.

Reviews on genome mining citing EvoMining

Medema, Marnix H., and Michael A. Fischbach. 2015. “Computational Approaches to Natural Product Discovery.” Nature Chemical Biology 11 (9): 639–48. doi:10.1038/nchembio.1884.

Ziemert, Nadine, Mohammad Alanjary, and Tilmann Weber. 2016. “ The Evolution of Genome Mining in Microbes – a Review. ” Natural Product Reports 33 (8): 988–1005. doi:10.1039/C6NP00025H.

Kim, Hyun Uk, Kai Blin, Sang Yup Lee, and Tilmann Weber. 2017. “Recent Development of Computational Resources for New Antibiotics Discovery.” Current Opinion in Microbiology 39 (October): 113–20. doi:10.1016/j.mib.2017.10.027.

Related links

The Secondary Metabolite Bioinformatics Portal

Evomining news

Quick EvoMining guide

1 Run evomining image

docker run -i -t -v $(pwd):/var/www/html/EvoMining/exchange -p 80:80 nselem/newevomining:latest /bin/bash

2 Run EvoMining on the docker container

perl startEvomining -g mygenomes -r myRastIds

3 View your results

If you are running EvoMining on your local machine.
http://localhost/html/EvoMining/index.html

or, if you are running EvoMining on a remote machine.
http://yourip/html/EvoMining/index.html
and follow EvoMining web interface steps.

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