/2018---2019-Equipe-2

Primary LanguagePython

MEET-U Upstream: team n°2

Foo

Our method

We are team n°2 from Paris Diderot. Here, we decide to make a profile-profile alignment in order to find a template which matches with a query. Our profile is composed by 20 amino-acids, gap and secondary structure informations. The alignment is a semi-global alignment and we made a dot-product score and a Pearson's correlation score. We will use those differents scores for our benchmark.

If you have any questions or problems, feel free to create an issue :)

Prerequisites

All the software and database you need :

Downloading database (ex: Uniref50) :

Dowload database here

Installing PSI-BLAST:

  • Install Legacy Blast : PSIBLAST 2.2.31+
    sudo apt-get install ncbi-blast+-legacy or conda install -c bioconda blast-legacy

Sometimes legacy blast need a perl library. Check if it needs it with running legacy blast

  • Formate database Uniref50
    formatdb -i uniref50.fasta -p T -o T

PSIPRED :

We give you the binary file of psipred, so you don't need to dowload it. But you need to download csh

sudo apt-get install csh

MAFFT :

Python 3 :

Python library :

pip install numpy
pip install pandas
pip install sys
pip install os
pip install glob

# Team 4 dependancies :
pip install docopt
pip install numpy
pip install biopython
pip install pandas
pip install schema
pip install tqdm
pip install matplotlib
pip install m2r

Team 4 dependancies :

sudo apt-get install dssp

conda install -c salilab modeller

How to use

Clone the repository :

git clone https://github.com/meetU-MasterStudents/2018---2019-Equipe-2.git

/!\ CHANGE DIRECTORY FOR DATABASE: in pipeline_final.sh

DIR_BD=/home/sdv/m2bi/dde_murat/MEET_U/BDD/uniref50.fasta

/!\ CHANGE DIRECTORY FOR DATABASE: in src/align_pssm.py

/home/madeleine/Documents/2018---2019-partage/Data/HOMSTRAD/

Lauch from directory : 2018---2019-Equipe-2

./pipeline_final.sh Query.fasta OUTPUT_FILE

Full pipeline UPSTREAM and DOWNSTREAM (launch from directory : 2018---2019-Equipe-2)

./pipeline_with_aval.sh Query.fasta OUTPUT_FILE

Example

./pipeline_with_aval.sh example/Cohesin.fasta Cohesin_output

Authors

  • Daniel DE MURAT - M2BI - Université Paris Diderot - DanielBI

  • Madeleine DE SOUSA-VIOLANTE - M2BI - Université Paris Diderot - madeleinevlt

  • Meishiue KUO - M2BI - Université Paris Diderot - meishiue

  • Sonia TIEO - M2BI - Université Paris Diderot - soniamaitieo