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.
start EvoMining on the prompt of the docker image with the default data by typing:
perl startEvoMining.pl
Once the script finished, 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, press the start button to initialize the web interface.
On a second screen EvoMining requires the e-value required to consider a sequence inside a family, default:0.001. Press submit button to launch the expansions script that for each enzymatic family identifies sequences belonging to the expanded family.
A heatmap table is presented to the user once the expanded family has been gathered. 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.
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.
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.
This is an example of a tree coming from a family that is non recruited.
This family is >3PGA_AMINOACIDS|1|Phosphoglycerate_dehydrogenase_1|Cglu
3PGA_AMINOACIDS|2|Phosphoserine_aminotransferase_3|none
Results are available at the terminal on path
ALL_curado.fasta_MiBIG_DB.faa_los17
This part explains how to use databases introduced by the user, 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 |
|---|---|
| los17 | Directory with the genome database |
| los17Rast.ids | Tab separated File with genome Names/Ids |
| central-DB.fasta | Central database file (fasta) |
| natural-DB.fasta | Natural products database |
-
Open a terminal and place your self on a local directory.
$ cd </path/to/mydirectory>
On the terminal prompt the starting character is$on the docker prompt the starting char is#. -
Start EvoMining docker image.
$ docker run -i -t -v $(pwd):/var/www/html/EvoMining/exchange -p 80:80 nselem/newevomining:latest /bin/bash
At this time the local directory /path/to/mydirectory and docker directory /var/www/html/EvoMining/exchange are shared.
- Move the sample data from the EvoMining docker into your local machine directory:
# cp -r /var/www/html/EvoMining/example/* /var/www/html/EvoMining/exchange/.
-Check that the data are correctly at your directory
$ ls /path/to/mydirectory
central-DB.fasta los17 los17Rast.ids natural-DB.fasta
-
Start EvoMining with non default databases
# perl startEvoMining.pl -g los17 -c central-DB.fasta -n natural-DB.fasta -r los17Rast.ids
This command starts EvoMining using as central-DB the file central-DB.fasta, as natural-DB natural-DB.fasta and as genome DB the genomes contained on the directory los17. It also needs the file los17Rast.ids that containes for each genome its name and its corresponding RAST id. To know more about how to construct you own databases conult Databases Conformation -
EvoMining browser
Open EvoMining web interface and follow the steps as on the prior example. -
Results
Results e.g. trees and alignments will be stored at/path/to/mydirectoryon the directory:
<central-DB>/<natural-DB>/<genome-DB>on this case this information correspondes to:
central-DB.fasta_natural-DB.fasta_los17
