How to Install and Uninstall sim4db Package on Ubuntu 20.10 (Groovy Gorilla)

Last updated: December 25,2024

1. Install "sim4db" package

This tutorial shows how to install sim4db on Ubuntu 20.10 (Groovy Gorilla)


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

Here is a brief guide to show you how to uninstall sim4db on Ubuntu 20.10 (Groovy Gorilla):


    
        
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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 20.10 (Groovy Gorilla)

Package: sim4db
Architecture: amd64
Version: 0~20150903+r2013-8
Priority: optional
Section: universe/science
Source: kmer
Origin: Ubuntu
Maintainer: Ubuntu Developers
Original-Maintainer: Debian Med Packaging Team
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 3340
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.0), libstdc++6 (>= 5.2)
Recommends: leaff, kmer-examples
Filename: pool/universe/k/kmer/sim4db_0~20150903+r2013-8_amd64.deb
Size: 435108
MD5sum: 0a1748d38ab13f7691d15aa723346fac
SHA1: 80fc3dd9a0404b2ebb023189efcff7cac89b6a65
SHA256: aaac3e1c7cae71dc0f92911f8490b2563b57aa06551e74101a0ebfb2c8a6f4ed
SHA512: 8d0b791d6d5107ec459ebfb6bd0fe5561979c62ee2a56ad565ea017d45eb9bdbb84f174871dde2547a96a2783ca62fc1ca944b214c25a8e4f888fd470dd959ba
Homepage: http://kmer.sourceforge.net
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.
.
This package is part of the Kmer suite.
Description-md5: 85f8fe3bbe88f71c2e69cb9b24788d42