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This is a python implementation of Statistical Coupling Analysis for bioinformatics

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What is this repository for?

What is SCA?

  • SCA is a computation technique to determine potential allosteric sites in protein families

  • based on evolutionary coupling between amino acid sequences in proteins.

  • Note that there is a lower bound on number of sequences used in an MSA determined by binomial

  • distribution of frequencies of amino acids and KL entropy function. Around 100 is what the

  • notes on SCA calculations suggest.

How do I get set up?

  • Summary of set up
  • Configuration
  • Dependencies: Procedure for Linux machines:
    1. SciPy has the following dependencies which need to be installed globally.

    2. Requirements.txt contains the list of the libraries/packages required.

The following commands can be used to install all the dependencies:

#!
sudo apt-get install gfortran libopenblas-dev liblapack-dev
pip install -r <location of requirements.txt file>

  • Database configuration
  • How to run tests
  • Deployment instructions

Contribution guidelines

  • Writing tests
  • Code review
  • Other guidelines

Who do I talk to?

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This is a python implementation of Statistical Coupling Analysis for bioinformatics

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