How To Install sim4 on Kali Linux

Introduction

In this tutorial we learn how to install sim4 on Kali Linux.

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 Kali Linux. 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 on Kali Linux first since aptitude is usually not installed by default on Kali Linux. 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 Kali Linux

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 Kali Linux, we can use the command below:

sudo apt-get -y autoremove sim4

Remove sim4 Configurations and Data

To remove sim4 configuration and data from Kali Linux 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:

• libc6

References

• sim4 website

Summary

In this tutorial we learn how to install sim4 package on Kali Linux using different package management tools: apt, apt-get and aptitude.