How To Install wise-data on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 545 words
Introduction
In this tutorial we learn how to install wise-data on Ubuntu.
What is wise-data
wise-data is:
Wise2 is a package focused on comparisons of biopolymers, commonly DNA and protein sequences. There are many other packages which do this, probably the best known being BLAST package (from NCBI) and the Fasta package (from Bill Pearson). There are other packages, such as the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused on hidden Markov models (HMMs) of biopolymers.
Wise2’s particular forte is the comparison of DNA sequence at the level of its protein translation. This comparison allows the simultaneous prediction of say gene structure with homology based alignment.
Wise2 also contains other algorithms, such as the venerable Smith-Waterman algorithm, or more modern ones such as Stephen Altschul’s generalised gap penalties, or even experimental ones developed in house, such as dba. The development of these algorithms is due to the ease of developing such algorithms in the environment used by Wise2.
Wise2 has also been written with an eye for reuse and maintainability. Although it is a pure C package you can access its functionality directly in Perl. Parts of the package (or the entire package) can be used by other C or C++ programs without namespace clashes as all externally linked variables have the unique identifier Wise2 prepended.
This package contains data files for Wise2, a package focused on comparisons of biopolymers, commonly DNA and protein sequences.
There are three methods to install wise-data on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install wise-data Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install wise-data using apt-get by running the following command:
sudo apt-get -y install wise-data
Install wise-data Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install wise-data using apt by running the following command:
sudo apt -y install wise-data
Install wise-data 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 Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install wise-data using aptitude by running the following command:
sudo aptitude -y install wise-data
How To Uninstall wise-data on Ubuntu
To uninstall only the wise-data package we can use the following command:
sudo apt-get remove wise-data
Uninstall wise-data And Its Dependencies
To uninstall wise-data and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove wise-data
Remove wise-data Configurations and Data
To remove wise-data configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge wise-data
Remove wise-data configuration, data, and all of its dependencies
We can use the following command to remove wise-data configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge wise-data
Dependencies
wise-data have the following dependencies:
References
Summary
In this tutorial we learn how to install wise-data package on Ubuntu using different package management tools: apt, apt-get and aptitude.