The source code for building the Yeast Mitochondrial PTM Database at http://compbio.fmph.uniba.sk/y-mtptm/

This repository contains scripts necessary to build the y-mtPTM database located at http://compbio.fmph.uniba.sk/y-mtptm/ Assuch, it is not really meant to be run by others, but it may help in setting up similar projects. Once generated, the whole website consists only of HTML, CSS and JavaScript files and does not require server-side computation.

How to run

Prerequisites:

• The software was tested only on linux systems
• Python version at least 3.8 is required
• Data files are downloaded via wget but alternatives such as curl can also be used
• Other necessary libraries and prerequisites are installed by conda

Downloading repository and setting up Python libraries:

git clone https://github.com/fmfi-compbio/y-mtptm.git

# change to src dir
cd y-mtptm/src

# install further prerequisites by conda
conda env create -f ../environment.yml
conda activate ymtptm

# all subsequent commands should be run in src folder
# and with conda environment activated

Downloading necessary data files:

# S. cerevisiae proteome fasta from Uniprot
cd ../data/uniprot
wget https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000002311/UP000002311_559292.fasta.gz
gunzip *.gz

# proteome fasta and gene names for SGD 
cd ../sgd
wget http://sgd-archive.yeastgenome.org/sequence/S288C_reference/orf_protein/archive/orf_trans_all_R64-3-1_20210421.fasta.gz
wget http://sgd-archive.yeastgenome.org/curation/literature/archive/gene_association.sgd.20210510.gaf.gz
gunzip *.gz

cd ../../src

Building the SQLite database from the Excel file:

• This will rewrite database provided in the repository but also download necessary pdb files

# remove the original database
rm ../data/excel/ymtptm.db
# create database schema
sqlite3 ../data/excel/ymtptm.db < create_db.sql
# fill database with data, download pdb files
# this takes some time
python3 excel_parser.py  2> excel.err > excel.log
# pdb files will be in ../data/pdb
# excel.err will contain some warnings

Building website from the SQLite database

# this command also takes longer time
python3 html_builder.py

This final step creates html files in ../web; these files can be then viewed in a browser locally or placed on a webserver.

The main files

• data/excel/*.xlsx Human readable Excel file with PTM data
• data/excel/ymtptm.db data in SQLite format
• data/excel/modifications.csv configuration file with all considered PTM types
• data/pdb folder for pdb files downloaded by excel_parser.py
• data/sgd folder for files from the SGD database
• data/uniprot folder for files from the Uniprot database
• web folder for the resulting website
• src/config.py filenames of data files
• src/create_db.sql SQLite database schema
• src/excel_parser.py script for converting database from Excel to SQLite
• src/html_builder.py script for building website from SQLite database
• src/templates HTML templates for jinja library
• src/web_include images and CSS files used on the website directly
• src/pdb_to_html files needed to convert pdb files for GLmol via pymol

The following files contain code originating from the GLmol package:

• src/pdb_to_html/pymol2glmol.py
• src/templates/protein_page.html
• src/web_include/glmol.js
• src/web_include/create_structure.js

Authors and license

The database content, source code and design of the website were created by Bronislava Brejová, Veronika Vozáriková, Ivan Agarský, Hana Derková, Matej Fedor, Dominika Harmanová, Lukáš Kiss, Andrej Korman, Martin Pašen, Filip Brázdovič, Jozef Nosek, Tomáš Vinař, Ľubomír Tomáška.

All of the authors were affiliated at the Faculty of Natural Sciences or the Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava.

Several files listed above contain modified code from the GLmol package by biochem_fan, which is distributed under the GNU Lesser General Public License. Therefore the whole repository y-mtptm is also distributed under this license.