How to Install and Uninstall sim4 Package on Ubuntu 20.10 (Groovy Gorilla)

Last updated: May 17,2024

1. Install "sim4" package

Please follow the guidance below to install sim4 on Ubuntu 20.10 (Groovy Gorilla)


    
        
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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 20.10 (Groovy Gorilla):


    
        
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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 20.10 (Groovy Gorilla)

Package: sim4
Architecture: amd64
Version: 0.0.20121010-5
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: 452
Depends: libc6 (>= 2.14)
Filename: pool/universe/s/sim4/sim4_0.0.20121010-5_amd64.deb
Size: 396616
MD5sum: d4aac7116a846fb41f2e3eae61e1ca53
SHA1: 1d356da42f92dbd281a03ee384c5ffb47bfbe21a
SHA256: 67b5e13212ec6a9c928eb9551c99eaeda195185af6acbbe39cc139bedc803924
SHA512: 363d8076b96fa5a74d246e22647971cf636073fc3041fb9e82f77b48afbe7c5a735ff28c3cad5da72956a20cf8826836a8a486f3da46bf5337aa120c35d5383c
Homepage: http://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