How To Install vienna-rna on Debian 12
Introduction
In this tutorial we learn how to install vienna-rna on Debian 12.
What is vienna-rna
vienna-rna is:
The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. It is developed and maintained by the group of Ivo Hofacker in Vienna.
RNA secondary structure prediction through energy minimization is the most used function in the package. It provides three kinds of dynamic programming algorithms for structure prediction:
- the minimum free energy algorithm of (Zuker & Stiegler 1981) which yields a single optimal structure,
- the partition function algorithm of (McCaskill 1990) which calculates base pair probabilities in the thermodynamic ensemble, and the suboptimal folding algorithm of (Wuchty et.al 1999) which generates all suboptimal structures within a given energy range of the optimal energy.
For secondary structure comparison, the package contains several measures of distance (dissimilarities) using either string alignment or tree-editing (Shapiro & Zhang 1990). Finally, is provided an algorithm to design sequences with a predefined structure (inverse folding). The RNAforester package is a tool for aligning RNA secondary structures and it’s user interface integrates to those of the tools of the Vienna RNA package.
There are three methods to install vienna-rna on Debian 12. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install vienna-rna Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install vienna-rna using apt-get by running the following command:
sudo apt-get -y install vienna-rna
Install vienna-rna Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install vienna-rna using apt by running the following command:
sudo apt -y install vienna-rna
Install vienna-rna 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 vienna-rna using aptitude by running the following command:
sudo aptitude -y install vienna-rna
How To Uninstall vienna-rna on Debian 12
To uninstall only the vienna-rna package we can use the following command:
sudo apt-get remove vienna-rna
Uninstall vienna-rna And Its Dependencies
To uninstall vienna-rna and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove vienna-rna
Remove vienna-rna Configurations and Data
To remove vienna-rna configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge vienna-rna
Remove vienna-rna configuration, data, and all of its dependencies
We can use the following command to remove vienna-rna configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge vienna-rna
Dependencies
vienna-rna have the following dependencies:
References
Summary
In this tutorial we learn how to install vienna-rna package on Debian 12 using different package management tools: apt, apt-get and aptitude.
