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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.
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Usage
Please consult Installation guide and Tutorial -
Introduction
Given a a family of enzymes EvoMining helps to recruitmennts of the expanded family into natural products biosynthetic gene cluster (BGCs) within 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] (http://148.247.230.39/newevomining/new/evomining_web/index.html) is a functional phylogenomics method for identification of expanded, re-purposed enzyme families, with the potential to catalyse new conversions in natural product biosynthesis.
[EvoMining: biosynthetic gene clusters allows discovery of arseno-organic metabolites] (http://gbe.oxfordjournals.org/content/early/2016/06/10/gbe.evw125.abstract)
[Evomining news] (https://codigof.mx/evomining-plataforma-bioinformatica-mexicano-desarrollar-nuevos-antibioticos/)
[Ziemert et al, June 2016] (http://pubs.rsc.org/en/Content/ArticleLanding/2016/NP/C6NP00025H#!divAbstract)
[Marnix & Fischbach, 2015] (http://www.nature.com/nchembio/journal/v11/n9/full/nchembio.1884.html)
[The Secondary Metabolite Bioinformatics Portal] (http://www.secondarymetabolites.org/mining/)
docker run -i -t -v $(pwd):/var/www/html/EvoMining/exchange -p 80:80 nselem/newevomining:latest /bin/bash
perl startevomining -g mygenomes -r myRastIds
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.
