How to Install and Uninstall pscan-chip Package on Ubuntu 21.10 (Impish Indri)

Last updated: May 16,2024

1. Install "pscan-chip" package

This guide covers the steps necessary to install pscan-chip on Ubuntu 21.10 (Impish Indri)


    
        
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                sudo apt update
            
                    
    
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                sudo apt install
            
                        
                pscan-chip
            
                    
    
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2. Uninstall "pscan-chip" package

This tutorial shows how to uninstall pscan-chip on Ubuntu 21.10 (Impish Indri):


    
        
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                sudo apt remove
            
                        
                pscan-chip
            
                    
    
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                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the pscan-chip package on Ubuntu 21.10 (Impish Indri)

Package: pscan-chip
Architecture: amd64
Version: 1.1-3
Priority: optional
Section: universe/science
Origin: Ubuntu
Maintainer: Ubuntu Developers
Original-Maintainer: Debian Med Packaging Team
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 188
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.0), libgsl25 (>= 2.6), libstdc++6 (>= 5.2)
Recommends: pscan-chip-data
Suggests: pscan-tfbs
Filename: pool/universe/p/pscan-chip/pscan-chip_1.1-3_amd64.deb
Size: 86024
MD5sum: 36e840fe73d179e50cf155de2e122be7
SHA1: 48e43b0581e5d2e48ec6948edb816f60bf00fc69
SHA256: baf9085c1c4ed6dbcbf8932fa0a21af1978cd0bcf03c191192eef39f7eb74fa5
SHA512: 7f8f8ef69cee54b0c841ecb90e843ed4e118d4074b4c663b76389e7ea01bfd0f7bc8017c833f02168fce85962628f2c33c92721aa4aedf60ca496eb6a2b629e4
Homepage: http://www.beaconlab.it/pscan_chip_dev/
Description-en: ChIP-based identifcation of TF binding sites
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).
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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.
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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.
Description-md5: 7d9dfc67111eeb94ca580e301b5b2847