How To Install toppred on Debian 12
Introduction
In this tutorial we learn how to install toppred on Debian 12.
What is toppred
toppred is:
Toppred is a program to determine the topology of a transmembrane protein based on G. von Heijne algorithm.
Each sequence from seq data in fasta format is processed, and toppred generate the Hydrophobycity profile of the sequence, and the corresponding hydrophobycities values in the file sequence-ID.hydro.
Furthermore, the predicted topologies are represented as png images. Each topology is stored in file sequence-ID-number.png
The hydrophobicity profile is computed using a window formed by a core rectangular window of size n, flanked by 2 triangular windows of size q. NB rectangular and triangular mean that the ponderation values inside those windows are respectively constant and variable.
This program is a new implementation of the original toppred program, based on G. von Heijne algorithm
There are three methods to install toppred 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 toppred Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install toppred using apt-get by running the following command:
sudo apt-get -y install toppred
Install toppred Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install toppred using apt by running the following command:
sudo apt -y install toppred
Install toppred 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 toppred using aptitude by running the following command:
sudo aptitude -y install toppred
How To Uninstall toppred on Debian 12
To uninstall only the toppred package we can use the following command:
sudo apt-get remove toppred
Uninstall toppred And Its Dependencies
To uninstall toppred and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove toppred
Remove toppred Configurations and Data
To remove toppred configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge toppred
Remove toppred configuration, data, and all of its dependencies
We can use the following command to remove toppred configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge toppred
Dependencies
toppred have the following dependencies:
References
Summary
In this tutorial we learn how to install toppred package on Debian 12 using different package management tools: apt, apt-get and aptitude.
