README

USER INFO

Instigator

name: Jean-Michel Garant

email: jean-michel.garant@usherbrooke.ca

gitlab username: J-Michel

REPO INFO

gitlab url: gitlabscottgroup.med.usherbrooke.ca/J-Michel/g4rna_screener

Version: G4RNA screener 0.3

Please consider cloning/downloading a stable branch

DEPENDENCIES

Here are listed dependencies in format:

library_name (recommended version)

From environment

python2.7 (2.7.15rc1)

From Python

Available from pip

biopython (1.68)
numpy (1.11.0)
pandas (0.18.1)
PyBrain (0.3)
regex (2016.9.22)
scipy (0.18.1)

mysql-connector-python (2.1.4) is also highly recommended for automated retrieval of information on UCSC and Ensembl databases using -c, --columns arguments. It is not available through pip but here are the steps to follow to install it:
sudo -i
cd PATH/TO/PYTHON/dist-packages/    or    cd PATH/TO/PYTHON/site-packages/
wget https://dev.mysql.com/get/Downloads/Connector-Python/mysql-connector-python-2.1.4.tar.gz --no-check-certificate
tar -xzf mysql-connector-python-2.1.4.tar.gz
cd mysql-connector-python-2.1.4
python setup.py install

Consider adding G4RNA screener to your environment path

Example for a bash terminal

cd PATH/TO/g4rna_screener
echo "" >> ~/.bashrc
echo "# add G4RNA screener to PATH" >> ~/.bashrc
echo "export PATH=\"\$PATH:$(pwd)\"" >> ~/.bashrc
source ~/.bashrc

GLOSSARY

ANN: Artificial Neural Network
AUC: Area Under ROC Curve
cGcC: consecutive guanine over consecutive cytosine, usually expressed as a score
csv: Comma separated values. A tabular text file readable by spreadsheet softwares such as Microsoft Excel and LibreOffice Calc. Files used in this project are actually .tsv (tab separated values) for better visualization in the terminal.
cv: Cross-validation
db: Database
DnB: Dot'n'Bracket notation for secondary structure
Ensembl: Joint project between European Bioinformatics Institute (EBI) and the Wellcome Trust Sanger Institute (WTSI)
fasta: File format for biological sequences
G4: G-quadruplex
G4RNA: G-quadruplex RNA database
NCBI: National Center for Biotechnology Information
mfe: Minimum free energy (kcal/mol)
mp2: Mammouth parallel 2
MySQL: Open Source SQL database management system from Oracle Corporation
nt: Nucleotide
PG4: Potential G-quadruplex
PRAC: Pavillon de Recherche Appliquée sur le Cancer de l'Université de Sherbrooke (Pavilion of Applied Research on Cancer)
PSQL: Open source object-relational database system
RefSeq: The Reference Sequence database of NCBI
regex: Regular expression
ROC: Receiver Operating Characteristic
RNA: RiboNucleic acid
UCSC: University of California in Santa Cruz

yqyang733/g4rna_screener