Example and sample data
On this tutorial are shown two EvoMining examples. 1) Utilizing default data, EvoMining web interface functionality is explained. 2)Use of custom input databases is exemplified with sample data. To learn more about how to construct the databases consult the databases site.
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After start EvoMining on the docker image with the default data by typing
perl startEvoMining.pl, start EvoMining web pipeline on firefox or any browser at the adress: http://localhost/html/EvoMining/index.html. When in doubt about how to launch EvoMining docker, consult Installation. This should be the welcome screen.
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Start expansions heat map. On a second screen EvoMining requires the e-value required to consider a sequence inside a family, default:0.001. Press start to launch the script that for each enzymatic family identifies sequences that belong to the extended family.
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Visualize expansions heatmap.
A heatmap table it is presented to the user. Organisms are distributed on the rows of the table. Each column represents an enzyme family. When an organism has a copy number above the average plus one standard deviation on one particular enzyme family, the correspondent square is filled in red, representing an expansion of that enzyme family on that particular organism. Once the heatmap is finished, continue to the search of genes of the family that has been recruited onto natural product biosynthetic gene clusters, press the submit button.
4.Natural Product recruitments table.
On this case, a table present for each family which natural products (NPs) are recruited an where this NPs where tested and deposited on MI-BiG. Select which enzyme family will be send to a phylogenetic reconstruction.
5.Selected trees finished
Once the phylogenetic history of an expanded family has been done, after alignment and curated, if it is enough information the trees that were able to generated are shown. Select a tree and send it to the visualization interface.
6.Visualizing trees
6.1 Non expanded tree.
This is an example of a tree coming from a family that is non recruited.
6.2 Expanded tree
ALL_curado.fasta_MiBIG_DB.faa_los10
This part explains how to use databases diferent from default, for that purpose this sample data will be used. There is no need to download the data because they are already included at the EvoMining docker.
Input sample data contains:
| File | Description |
|---|---|
| los10 | Directory with the genome database |
| Rast.los10perl | Tab separated File with genome Names/Ids |
| mycent_los10 | Central database file (fasta) |
| my_nat_los10 | Natural products database |
Place your self on a folder
After starting EvoMining docker image.
$ docker run -i -t -v $(pwd):/var/www/html/EvoMining/exchange -p 80:80 nselem/newevomining:latest /bin/bash
There are a sampla data preloaded on EvoMining docker.
Move this data into your local machine directory:
cp -r /var/www/html/EvoMining/example/* /var/www/html/EvoMining/exchange/.
This instruction move the content of the example folder inside the docker container into
los10 mycent_los10 my_nat_los10 Rast.los10
los10 mycent_los10 mycent_los10_my_nat_los10_los10 my_nat_los10 Rast.los10perl startEvoMining.pl -g los10 -c mycent_los10 -n my_nat_los10 -r Rast.los10
