How to Install and Uninstall sim4 Package on Ubuntu 21.10 (Impish Indri)

Last updated: May 08,2024

1. Install "sim4" package

This guide let you learn how to install sim4 on Ubuntu 21.10 (Impish Indri)


    
        
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                sudo apt update
            
                    
    
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                sudo apt install
            
                        
                sim4
            
                    
    
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2. Uninstall "sim4" package

Please follow the instructions below to uninstall sim4 on Ubuntu 21.10 (Impish Indri):


    
        
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                sudo apt remove
            
                        
                sim4
            
                    
    
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                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the sim4 package on Ubuntu 21.10 (Impish Indri)

Package: sim4
Architecture: amd64
Version: 0.0.20121010-8
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: 1374
Depends: libc6 (>= 2.29)
Filename: pool/universe/s/sim4/sim4_0.0.20121010-8_amd64.deb
Size: 359644
MD5sum: 79d862cd414f18a74ddc61069668d32b
SHA1: d933662fbc68e6c84eb7ae2724ca0e47a219dfe3
SHA256: c70d75d7aad3919de55fadea51ee6884390ceea9dd3bbd0994139b0efcbea260
SHA512: 1eba93409ad79f8b8f83493f50855bfc2e7f6c9673b3a438445b7e153702af7fffe52583f999fb84dbdc2ffaf44425529c724a3b8d80c49d3159063ae248fdf5
Homepage: https://globin.bx.psu.edu/html/docs/sim4.html
Description-en: tool for aligning cDNA and genomic DNA
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).
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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.
Description-md5: 0707bae1b16add47eb5b50ce765a58ec