How to Install and Uninstall sim4db Package on Ubuntu 16.04 LTS (Xenial Xerus)

Last updated: May 17,2024

1. Install "sim4db" package

Please follow the step by step instructions below to install sim4db on Ubuntu 16.04 LTS (Xenial Xerus)


    
        
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                sudo apt update
            
                    
    
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                sudo apt install
            
                        
                sim4db
            
                    
    
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2. Uninstall "sim4db" package

Please follow the guidelines below to uninstall sim4db on Ubuntu 16.04 LTS (Xenial Xerus):


    
        
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                sudo apt remove
            
                        
                sim4db
            
                    
    
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                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the sim4db package on Ubuntu 16.04 LTS (Xenial Xerus)

Package: sim4db
Priority: optional
Section: universe/science
Installed-Size: 3253
Maintainer: Ubuntu Developers
Original-Maintainer: Debian Med Packaging Team
Architecture: amd64
Source: kmer-tools
Version: 0~20150903+r2013-1
Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), libstdc++6 (>= 5.2)
Recommends: leaff
Filename: pool/universe/k/kmer-tools/sim4db_0~20150903+r2013-1_amd64.deb
Size: 439320
MD5sum: 39a4834ebb8ead25b31d5fc116242d3f
SHA1: 1ca6aed5679b23c625cc9da34182490269111d20
SHA256: 9e658c10fc670c771b778e21ce26c2efb4e89b7eb0a194bf3109f56829c764a1
Description-en: batch spliced alignment of cDNA sequences to a target genome
Sim4db performs fast batch alignment of large cDNA (EST, mRNA) sequence
sets to a set of eukaryotic genomic regions. It uses the sim4 and sim4cc
algorithms to determine the alignments, but incorporates a fast sequence
indexing and retrieval mechanism, implemented in the sister package
'leaff', to speedily process large volumes of sequences.
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While sim4db produces alignments in the same way as sim4 or sim4cc, it
has additional features to make it more amenable for use with whole-genome
annotation pipelines. A script file can be used to group pairings between
cDNAs and their corresponding genomic regions, to be aligned as one run
and using the same set of parameters. Sim4db also optionally reports more
than one alignment for the same cDNA within a genomic region, as long
as they meet user-defined criteria such as minimum length, percentage
sequence identity or coverage. This feature is instrumental in finding
all alignments of a gene family at one locus. Lastly, the output is
presented either as custom sim4db alignments or as GFF3 gene features.
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This package is part of the Kmer suite.
Description-md5: 85f8fe3bbe88f71c2e69cb9b24788d42
Homepage: http://kmer.sourceforge.net
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Origin: Ubuntu