How To Install sim4 on Debian 9
Introduction
In this tutorial we learn how to install sim4 on Debian 9.
What is sim4
sim4 is:
sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects end matches when the two input sequences overlap at one end (i.e., the start of one sequence overlaps the end of the other).
sim4 employs a blast-based technique to first determine the basic matching blocks representing the “exon cores”. In this first stage, it detects all possible exact matches of W-mers (i.e., DNA words of size W) between the two sequences and extends them to maximal scoring gap-free segments. In the second stage, the exon cores are extended into the adjacent as-yet-unmatched fragments using greedy alignment algorithms, and heuristics are used to favor configurations that conform to the splice-site recognition signals (GT-AG, CT-AC). If necessary, the process is repeated with less stringent parameters on the unmatched fragments.
There are three methods to install sim4 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 sim4 Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install sim4 using apt-get by running the following command:
sudo apt-get -y install sim4
Install sim4 Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install sim4 using apt by running the following command:
sudo apt -y install sim4
Install sim4 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 sim4 using aptitude by running the following command:
sudo aptitude -y install sim4
How To Uninstall sim4 on Debian 9
To uninstall only the sim4 package we can use the following command:
sudo apt-get remove sim4
Uninstall sim4 And Its Dependencies
To uninstall sim4 and its dependencies that are no longer needed by Debian 9, we can use the command below:
sudo apt-get -y autoremove sim4
Remove sim4 Configurations and Data
To remove sim4 configuration and data from Debian 9 we can use the following command:
sudo apt-get -y purge sim4
Remove sim4 configuration, data, and all of its dependencies
We can use the following command to remove sim4 configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge sim4
Dependencies
sim4 have the following dependencies:
References
Summary
In this tutorial we learn how to install sim4 package on Debian 9 using different package management tools: apt, apt-get and aptitude.