A tool to model the evolution and structural impact of alternative splicing

Status	Linux, OSX	Windows

PhyloSofS (Phylogenies of Splicing isoforms Structures) is a fully automated computational tool that infers plausible evolutionary scenarios explaining a set of transcripts observed in several species and models the three-dimensional structures of the produced protein isoforms.
The phylogenetic reconstruction algorithm relies on a combinatorial approach and the maximum parsimony principle. The generation of the isoforms' 3D models is performed using comparative modeling.

PhyloSofS was applied to the c-Jun N-terminal kinase (JNK) family (60 transcripts in 7 species). It enabled to date the appearance of an alternative splicing event (ASE) resulting in substrate affinity modulation in the ancestor common to mammals, amphibians and fishes, and to identify key residues responsible for such modulation. It also highlighted a new ASE inducing a large deletion, yet conserved across several species. The resulting isoform is stable in solution and could play a role in the cell. More details about this case study, together with the algorithm description, can be found in the PhyloSofS' preprint available at bioRxiv.

You can clone this PhyloSofS package using git:

git clone https://github.com/PhyloSofS-Team/PhyloSofS.git

Then, you can access the cloned PhyloSofS folder and install the package using Python 3's pip:

cd PhyloSofS
python -m pip install .

To run the phylogenetic module of PhyloSofS, you need to have Graphviz installed.
The easiest way to install Graphviz in...

• Debian/Ubuntu is: sudo apt-get install graphviz
• Windows is using Chocolatey: choco install graphviz
• macOS is using Homebrew: brew install graphviz

The molecular modelling pipeline depends on Julia, HH-suite3 and MODELLER. This module can only run on Unix systems (because of the HH-suite). To alleviate that, we offer a Docker image with all these dependencies installed (see the Docker section for more details).

You can download Julia 1.1.1 binaries from its site. Once, Julia is installed, open the REPL and install the needed packages by doing:

using Pkg
Pkg.add(["MIToS", "Statistics", "CSV", "Plots", "StatsPlots", "DataFrames", "BioAlignments", "BioStructures"])

Some BioJulia packages can need LibZ to precompile. If you found a related error, you can install LibZ from its site. In Ubuntu 18.04 you can install it by doing: sudo apt-get install zlib1g-dev

Clone our HH-suite fork at AntoineLabeeuw/hh-suite and follow the Compilation instructions in its README.md file.

PhyloSofS needs MODELLER version 9.21. Follow the instructions in the MODELLER site to install it and get the license key.

To run the molecular modelling module you need the sequence database for HH-suite3 and the structural database (PDB) for MODELLER. Follow the instructions in docs/get_databases.md to set them up.

To run PhyloSofS' Docker image you need to install Docker from the Docker website.

The following example is going to run PhyloSofS' Docker image using Windows PowerShell. Databases for the molecular modelling module stored in D:\databases are going to be mounted in /databases and the local directory in /project. The actual folder is ${PWD} in Windows PowerShell, %cd% in Windows Command Line (cmd), and $(pwd) in Unix.

docker run -ti --rm --mount type=bind,source=d:\databases,target=/databases --mount type=bind,source=${PWD},target=/project diegozea/phylosofs

After this, we have access to the bash terminal of an Ubuntu 18.04 image with PhyloSofS and all its dependencies installed. You only need to indicate your MODELLER license key to use PhyloSofS. To do that, you run the following command after replacing license_key with your MODELLER license key:

sed -i 's/xxx/license_key/' /usr/lib/modeller9.21/modlib/modeller/config.py

If you are using the PhyloSofS' Docker image, you must know that errors can occur when very large files are being written to bind-mounted NTFS file systems. This happens particularly when setup_databases is run because it tries to download and decompress large files. To avoid this problem, you can install PhyloSofS on Windows and run setup_databases.exe to set up the databases before using the docker image.

You can run phylosofs -h to see the help and the list of arguments.

phylosofs -P -s 100 --tree path_to_newick_tree --transcripts path_to_transcripts

phylosofs  -M -i path_to_input_files --hhlib path_to_hhsuite_folder --hhdb path_to_hblits_database(uniclust30)/basename --structdb path_to_hhpred(pdb70)/basename --allpdb path_to_the_cif_database --ncpu number_of_cpu --julia path_to_julia_executable

Please note that for the databases hhdb and structdb, you need to provide the path to the folder and also the base name of the files in it. For example, if the database uniclust30_2018_08 is located in /home, you need to write --hhdb /home/uniclust30_2018_08/uniclust30_2018_08

phylosofs -M -i . --hhlib /app/hh-suite/ --hhdb /databases/uniclust30_2018_08/uniclust30_2018_08 --structdb /databases/pdb70_from_mmcif_latest/pdb70 --allpdb /databases/allpdb/ --ncpu 12

The PhyloSofS package has been developed under the MIT License.

For questions, comments or suggestions feel free to contact Elodie Laine or Hugues Richard