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Add Phylogenomics data

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drbecavin edited this page May 25, 2020 · 17 revisions

The second bacnet.e4.rap.setup panel helps you create a phylogenomics tree figure, using JolyTree, of the different genomes listed in genomes.txt file. This tree will be displayed in the final website and used to reorder genome list in the corrected phylogeny related order.

An homolog search tool is also available to complete the phylogenomics study. You can run an external script using BlastP search for comparison of all annotated proteins in all genomes. Then a Bacnet internal script will summarize Blast results and select best homolog hit for each protein in each genome. Thus, in your multiomics website, you will be able to display all homologs of a gene through all listed genomes in the gene visualization panel.

Creation of the phylogenomic tree

If you don't already have a .svg phylogenomic tree in the Annotation folder of your database you need to create it. To do so click on Run Phylogenomic tree creation. Details on the next steps should be written in the console. Install JolyTree either using https://gitlab.pasteur.fr/GIPhy/JolyTree or directly use the one in bacnet.e4.rap.setup. To use it you will need to install some dependencies on your computer: mash (Ondov et al. 2016) version >= 1.0.2, gawk version >= 4.1.0, FastME (Lefort et al. 2015) version >= 2.1.5.1, REQ version >= 1.2.

Installation of needed packages (Linux or MAC-OS)

To facilitate their installation go to anaconda.org website, search for the dependency name and use the command line given.

Installation of needed packages (Windows)

Some of the dependencies are not available on Windows. Therefore you will need to install Windows Subsystem Linux to enable Linux packages to work.

  1. On your Start Menu open turn Windows features on and off and check the box Windows Subsystem for Linux (Beta). Press OK then restart your computer.
  2. Install your WSL desired distribution through the Windows Store (e.g.: Ubuntu 16.04 LTS), once it's downloaded open it. The completing of the installation once the distribution launched can take a few minutes.
  3. Once it's completed you will be asked to choose a username and a password.
  4. To update the packages of your distribution (not automatically done on Windows) launch the commands sudo apt update and sudo apt upgrade.
  5. All the command needed for phylogeny will be launched through MobaXterm interface. Download it and open it. Make sure the Xserver (top right corner) is launched.
  6. Launch a new WSL session: click on Sessions > New Session, on the window that opened click on Shell and select your WSL distribution for Terminal Shell and click OK. Capture_d_écran__16_
  7. Install the different packages through this WSL session by launching the commands "sudo apt install packagename".
  8. To access the usual Windows drives through your WSL session you need to type "cd /mtn/" and they should be accessible.

Next steps (for any OS)

  1. Launch the creation of the tree using: "JolyTree.sh -i D:\Programming\GitRepository\ListeriomicsSample\GenomeNCBI\Fasta/ -b PhylogenyGenomes" and copy the results in D:\Programming\GitRepository\ListeriomicsSample\Temp_.

  2. Next you need to install FigTree on your computer by going to http://tree.bio.ed.ac.uk/software/figtree/. Run FigTree and load the file PhylogenyGenomes.nwk that you created with JolyTree. (see ListeriomicsSample/GenomeNCBI/Homologs/)

  3. To create your final phylogenomic tree select Align Tip Labels and Trees>Transform branches>Proportional, resize labels in Tip Labels>Font Size and resize FigTree to have a vertical image. Save the figure in D:\Programming\GitRepository\ListeriomicsSample\Database\Annotation\PhylogenyGenomes.svg so that BACNET interface can access it.

(We have added 3 other genomes in ListeriomicsSample to be able to create the phylogenomicTree. remove them when creating your own database)

Once your phylogenomic tree is created and available you can order the genomes table. For this click on Organize genome table with phylogenomic tree.

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If everything went well you can now deploy "bacnet.e4.rap" by running it on Eclipse. Go to Genomics tool, you should obtain the list of genomes and the corresponding phylogenomic tree.

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Now pursue on the same panel to perform Homolog search.

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