How To Install conservation-code on Debian 9

In this tutorial we learn how to install conservation-code on Debian 9. conservation-code is protein sequence conservation scoring tool

Introduction

In this tutorial we learn how to install conservation-code on Debian 9.

What is conservation-code

conservation-code is:

This package provides score_conservation(1), a tool to score protein sequence conservation.

The following conservation scoring methods are implemented:

  • sum of pairs
  • weighted sum of pairs
  • Shannon entropy
  • Shannon entropy with property groupings (Mirny and Shakhnovich 1995, Valdar and Thornton 2001)
  • relative entropy with property groupings (Williamson 1995)
  • von Neumann entropy (Caffrey et al 2004)
  • relative entropy (Samudrala and Wang 2006)
  • Jensen-Shannon divergence (Capra and Singh 2007)

A window-based extension that incorporates the estimated conservation of sequentially adjacent residues into the score for each column is also given. This window approach can be applied to any of the conservation scoring methods.

The program accepts alignments in the CLUSTAL and FASTA formats.

The sequence-specific output can be used as the conservation input for concavity.

Conservation is highly predictive in identifying catalytic sites and residues near bound ligands.

There are three methods to install conservation-code on Debian 9. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install conservation-code Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install conservation-code using apt-get by running the following command:

sudo apt-get -y install conservation-code

Install conservation-code Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install conservation-code using apt by running the following command:

sudo apt -y install conservation-code

Install conservation-code Using aptitude

If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Debian. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install conservation-code using aptitude by running the following command:

sudo aptitude -y install conservation-code

How To Uninstall conservation-code on Debian 9

To uninstall only the conservation-code package we can use the following command:

sudo apt-get remove conservation-code

Uninstall conservation-code And Its Dependencies

To uninstall conservation-code and its dependencies that are no longer needed by Debian 9, we can use the command below:

sudo apt-get -y autoremove conservation-code

Remove conservation-code Configurations and Data

To remove conservation-code configuration and data from Debian 9 we can use the following command:

sudo apt-get -y purge conservation-code

Remove conservation-code configuration, data, and all of its dependencies

We can use the following command to remove conservation-code configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge conservation-code

Dependencies

conservation-code have the following dependencies:

References

Summary

In this tutorial we learn how to install conservation-code package on Debian 9 using different package management tools: apt, apt-get and aptitude.