How to Install and Uninstall sim4db Package on Ubuntu 21.10 (Impish Indri)

Last updated: November 24,2024

1. Install "sim4db" package

Please follow the guidelines below to install sim4db on Ubuntu 21.10 (Impish Indri)


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

Learn how to uninstall sim4db on Ubuntu 21.10 (Impish Indri):


    
        
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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 21.10 (Impish Indri)

Package: sim4db
Architecture: amd64
Version: 0~20150903+r2013-8build1
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: 3364
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.0), libstdc++6 (>= 5.2)
Recommends: leaff, kmer-examples
Filename: pool/universe/k/kmer/sim4db_0~20150903+r2013-8build1_amd64.deb
Size: 438172
MD5sum: 6b0379a43a13c2d85d10a472afe748d1
SHA1: 87619ddf029a03c932607d7d3adaa4870c6064ce
SHA256: c914f210275ede9748d7ce031446c7736f85bdf0d8e8dcc3a3aad247b6095b40
SHA512: fcb12caa5bf30783af40e60a23712677683b3db19ad5d4fd6b34c733c0a3c97bcd5e7c6ff90d7bd2d88deaba4b7239bd5449bd9e0b23729d8f5ff0f50f18ce25
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.
.
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