Genome DB

Genome Databases

EvoMining docker applications comes with a demo set of 17 Actinobacteria genomes. This genomes comes from NCBI, they were annotated on RAST and their protein file (faa) and RAST annotation were used on this pipeline. In order to distinguish from antismash hits, this genomes were previously explored on antiSMASH for natural biosynthetic clusters, but this step is not necessary for the pipeline

Construct your own Genome Database

In order to explore your own genomes using evoMining pipeline, follow this instructions.

1. Annotate your genomes on RAST.

Upload your genomes either fasta or gbk format to RAST annotator. Docker application docker-myrast may be used to upload them on batch.

2. Download you genomes and place them on a folder, this directory will be called your volume.

Genomes can be download from RAST directly at the web site or using docker-myrast application.
mkdir /home/mydir
mv *.faa /home/mydir
mv *.txt /home/mydyr
mv RAST.IDs /home/mydir

3. Pass this volume to evomining using the modifier -v when runing docker EvoMining.

docker run -i -t -v /home/mydyr/:/var/www/html -p 80:80 newevomining /bin/bash

4. Set your database as the Genomic Database.

run script setDB (pendent)
setDB must do: Rast_to_Evo cat *faa > myfolder.fasta
mv myfolder.faa DB/myfolder
perl -p-i-e 's/=".+"/="myfolder"/ if /GENOME/' globals.pm
perl reparaheader.pl

Inside directory DB mkdyr myDB
myDB.fasta

Where myDB.fasta is a fasta file with all your genomes on evomining format

1. Downloaded from RAST
2. RAST to evo script