How to Install and Uninstall sim4 Package on Ubuntu 16.04 LTS (Xenial Xerus)

Last updated: May 17,2024

1. Install "sim4" package

Please follow the instructions below to install sim4 on Ubuntu 16.04 LTS (Xenial Xerus)


    
        
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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 guidance below to uninstall sim4 on Ubuntu 16.04 LTS (Xenial Xerus):


    
        
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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 16.04 LTS (Xenial Xerus)

Package: sim4
Priority: optional
Section: universe/science
Installed-Size: 108
Maintainer: Ubuntu Developers
Original-Maintainer: Debian Med Packaging Team
Architecture: amd64
Version: 0.0.20121010-2
Depends: libc6 (>= 2.14)
Filename: pool/universe/s/sim4/sim4_0.0.20121010-2_amd64.deb
Size: 50736
MD5sum: aa826d13df9b2a4bf510189bb6a40db2
SHA1: 366131ca62691592ecad1b5c13721dafa4adfdf5
SHA256: 6cf127374d016a57fa2dcc905e2eb3ff4eb1162d862eaa61fdda1666e14659ab
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
Homepage: http://globin.bx.psu.edu/html/docs/sim4.html
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Origin: Ubuntu