How to Install and Uninstall conservation-code Package on Ubuntu 21.10 (Impish Indri)

Last updated: November 25,2024

1. Install "conservation-code" package

Learn how to install conservation-code on Ubuntu 21.10 (Impish Indri)


    
        
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                sudo apt update
            
                    
    
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            $
        

        
            
                sudo apt install
            
                        
                conservation-code
            
                    
    
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2. Uninstall "conservation-code" package

In this section, we are going to explain the necessary steps to uninstall conservation-code on Ubuntu 21.10 (Impish Indri):


    
        
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                sudo apt remove
            
                        
                conservation-code
            
                    
    
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            $
        

        
            
                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the conservation-code package on Ubuntu 21.10 (Impish Indri)

Package: conservation-code
Architecture: all
Version: 20110309.0-8
Priority: extra
Section: universe/science
Origin: Ubuntu
Maintainer: Ubuntu Developers
Original-Maintainer: Debian Med Packaging Team
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 114
Depends: python3:any, python3-numpy
Enhances: concavity
Filename: pool/universe/c/conservation-code/conservation-code_20110309.0-8_all.deb
Size: 23748
MD5sum: f3d47f26b026fc166bf60668e97f8b27
SHA1: 8aa44e5e333d8e8dfa47c182850a6785825a4378
SHA256: de57b11105cae584cf08713861a1d4a4f7e619c4edda4d86cb34cb12514bcb43
SHA512: 211788b7ff7569ba376a6bbebbc0f888d94a9603410fe1b384d66bbe5029fce18fdfbcbcd720715d82b9b322dc64b863db616f8d18d14cdd8af6582f43909102
Homepage: https://compbio.cs.princeton.edu/conservation/
Description-en: protein sequence conservation scoring tool
This package provides score_conservation(1), a tool to score protein sequence
conservation.
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The following conservation scoring methods are implemented:
* sum of pairs
* weighted sum of pairs
* Shannon entropy
* Shannon entropy with property groupings (Mirny and Shakhnovich 1995,
Valdar and Thornton 2001)
* relative entropy with property groupings (Williamson 1995)
* von Neumann entropy (Caffrey et al 2004)
* relative entropy (Samudrala and Wang 2006)
* Jensen-Shannon divergence (Capra and Singh 2007)
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A window-based extension that incorporates the estimated conservation of
sequentially adjacent residues into the score for each column is also given.
This window approach can be applied to any of the conservation scoring
methods.
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The program accepts alignments in the CLUSTAL and FASTA formats.
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The sequence-specific output can be used as the conservation input for
concavity.
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Conservation is highly predictive in identifying catalytic sites and
residues near bound ligands.
Description-md5: 35f238c6a81ce482741e5d5359932062