How to Install and Uninstall sim4 Package on Kali Linux

Last updated: May 17,2024

1. Install "sim4" package

This guide covers the steps necessary to install sim4 on Kali Linux


    
        
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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 Kali Linux:


    
        
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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 Kali Linux

Package: sim4
Version: 0.0.20121010-8
Installed-Size: 1371
Maintainer: Debian Med Packaging Team
Architecture: amd64
Depends: libc6 (>= 2.29)
Size: 359260
SHA256: de3b62e4951263055d164276ce807e83b1979d7e2b234ab2885e9483b0397efd
SHA1: 2abe3074f87c40d98febca121def748e15c52a53
MD5sum: 0a5ad2397e0629ff19ef3ec14764d5dd
Description: 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:
Homepage: https://globin.bx.psu.edu/html/docs/sim4.html
Tag: field::biology, field::biology:bioinformatics, implemented-in::c,
interface::commandline, role::program, scope::utility, use::comparing,
use::searching, works-with-format::TODO, works-with-format::plaintext,
works-with::TODO
Section: science
Priority: optional
Filename: pool/main/s/sim4/sim4_0.0.20121010-8_amd64.deb