How To Install pscan-chip on Kali Linux

Introduction

In this tutorial we learn how to install pscan-chip on Kali Linux.

What is pscan-chip

pscan-chip is:

Regulation of transcription is one of the main check points of gene expression regulation and plays a key role in fundamental processes like cellular differentiation and dynamic molecular responses to stimuli The transcriptional activity of genes is finely regulated by the interaction of sequence elements on the DNA (transcription factor binding sites or TFBSs) and particular proteins called Transcription Factors (TFs). , TFBSs are usually clustered in specific regulatory genomic regions called promoters and enhancers. TFs usually recognize TFBSs in a loose sequence specific fashion but there is no computational way to determine if any given sequence motif on the DNA is actually bound in-vivo by a TF, even when the motif is an istance of the sequences typically bound by the TF itself.

Tools like Pscan and PscanChIP analyse a set of regulatory sequences to detect motif enrichment. The rationale is that if a given TFBS is present in a “surpisingly high” number of istances then there is a good chance that the TF that recognize that motif is a common regulator of the input sequences, thus they use redundancy as an information source.

While Pscan (of the pscan-tfbs package) is tailored to work on promoters, that is the regulatory regions upstream of transcription start sites, PscanChIP is suited to work on more general regulatory genomic regions like the ones identified through ChIP-Seq experiments.

There are three methods to install pscan-chip 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 pscan-chip Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install pscan-chip using apt-get by running the following command:

sudo apt-get -y install pscan-chip

Install pscan-chip Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install pscan-chip using apt by running the following command:

sudo apt -y install pscan-chip

Install pscan-chip 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 pscan-chip using aptitude by running the following command:

sudo aptitude -y install pscan-chip

How To Uninstall pscan-chip on Kali Linux

To uninstall only the pscan-chip package we can use the following command:

sudo apt-get remove pscan-chip

Uninstall pscan-chip And Its Dependencies

To uninstall pscan-chip and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove pscan-chip

Remove pscan-chip Configurations and Data

To remove pscan-chip configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge pscan-chip

Remove pscan-chip configuration, data, and all of its dependencies

We can use the following command to remove pscan-chip configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge pscan-chip

Dependencies

pscan-chip have the following dependencies:

• libc6
• libgcc-s1
• libgsl25
• libstdc++6

References

• pscan-chip website

Summary

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