perl-Bio-CUA-1.04-alt1.noarch.rpm


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Description

perl-Bio-CUA - Codon Usage Analyzer

Property Value
Distribution ALT Linux Sisyphus
Repository Autoimports noarch
Package name perl-Bio-CUA
Package version 1.04
Package release alt1
Package architecture noarch
Package type rpm
Installed size 147.67 KB
Download size 147.67 KB
Official Mirror ftp.altlinux.org
The aim of this distribution is to provide comprehensive and flexible
tools to analyze codon usage bias (CUB) and relevant problems, so that
users can speed up the genetic research by taking advantage of this
convenience.
One amino acid can be encoded by more than one synonymous codon, and
synonymous codons are unevenly used. For example, some codons are used
more often than other synonymous ones in highly expressed genes (*Sharp
and Li 1987*). To measure the unevenness of codon usage, multiple
metrics of codon usage bias have been developed, such as Fop
(Frequency of optimal codons), CAI (Codon Adaptation Index), tAI (tRNA
Adaptation Index), and ENC (Effective Number of Codons). The causes of
CUB phenomena are complicated, including, mutational bias, selection on
translational efficiency or accurancy. CUB is one fundamental concept
in genetics.
So far, no software exists to compute all the above CUB metrics, and
more importantly parameters of CUB calculations are often fixed in
software, so one can only analyze genes in a limited list of species
and one can not incorporate its own parameters such as sequences of
highly expressed genes in a tissue.
This package mainly solves these two problems. We also extend some
methods, such as GC-content corrected ENC, background-data normalized
CAI, etc. See the relevant methods in CUB classes for more details.

Alternatives

Package Version Architecture Repository
perl-Bio-CUA - - -

Requires

Name Value
/usr/share/perl5 -
perl(Bio/SeqIO.pm) -
perl(Scalar/Util.pm) -
perl(base.pm) -
perl(parent.pm) -
rpmlib(PayloadIsLzma) -

Provides

Name Value
perl(Bio/CUA.pm) = 1.040
perl(Bio/CUA/CUB.pm) -
perl(Bio/CUA/CUB/Builder.pm) -
perl(Bio/CUA/CUB/Calculator.pm) -
perl(Bio/CUA/CodonTable.pm) -
perl(Bio/CUA/Seq.pm) -
perl(Bio/CUA/SeqIO.pm) -
perl(Bio/CUA/Summarizer.pm) -
perl-Bio-CUA = 1.04-alt1

Download

Type URL
Binary Package perl-Bio-CUA-1.04-alt1.noarch.rpm
Source Package perl-Bio-CUA-1.04-alt1.src.rpm

Install Howto

  1. Add the following line to /etc/apt/sources.list:
    
    rpm [Sisyphus] http://ftp.altlinux.org/pub/distributions/ALTLinux/autoimports/Sisyphus noarch autoimports
    rpm [Sisyphus] http://ftp.altlinux.org/pub/distributions/ALTLinux/autoimports/Sisyphus noarch autoimports
    
  2. Update the package index:
    # sudo apt-get update
  3. Install perl-Bio-CUA rpm package:
    # sudo apt-get install perl-Bio-CUA

Files

Path
/usr/share/doc/perl-Bio-CUA-1.04/Changes
/usr/share/doc/perl-Bio-CUA-1.04/LICENSE
/usr/share/doc/perl-Bio-CUA-1.04/README
/usr/share/doc/perl-Bio-CUA-1.04/TODO
/usr/share/perl5/Bio/CUA.pm
/usr/share/perl5/Bio/CUA/CUB.pm
/usr/share/perl5/Bio/CUA/CodonTable.pm
/usr/share/perl5/Bio/CUA/Seq.pm
/usr/share/perl5/Bio/CUA/SeqIO.pm
/usr/share/perl5/Bio/CUA/Summarizer.pm
/usr/share/perl5/Bio/CUA/Tutorial.pod
/usr/share/perl5/Bio/CUA/CUB/Builder.pm
/usr/share/perl5/Bio/CUA/CUB/Calculator.pm

See Also

Package Description
perl-Bio-CUA-scripts-1.04-alt1.noarch.rpm Bio-CUA scripts
perl-Bio-Cellucidate-0.03-alt1.noarch.rpm Perl library for cellucidate.com
perl-Bio-Chado-Schema-0.20000-alt1.noarch.rpm A standard DBIx::Class layer for the Chado database schema
perl-Bio-Cigar-1.01-alt1.noarch.rpm Parse CIGAR strings and translate coordinates to/from reference/query
perl-Bio-DB-NextProt-1.05-alt1.noarch.rpm Object interface to NextProt REST API
perl-Bio-DB-USeq-0.24-alt1.noarch.rpm Read USeq archive database files
perl-Bio-DB-USeq-scripts-0.24-alt1.noarch.rpm Bio-DB-USeq scripts
perl-Bio-DNA-Incomplete-0.004-alt1.noarch.rpm Match incompletely specified bases in nucleic acid sequences
perl-Bio-DOOP-DOOP-1.04-alt1.noarch.rpm DOOP API main module
perl-Bio-Das-1.17-alt1.noarch.rpm Client-side library for Distributed Genome Annotation System
perl-Bio-Das-Lite-2.11-alt1.noarch.rpm Bio::Das::Lite is an implementation of the BioDas protocol, http://biodas.org/
perl-Bio-EBI-RNAseqAPI-1.04-alt1.noarch.rpm A Perl interface to the EMBL-EBI RNA-seq analysis API
perl-Bio-ECell-0.10-alt1.noarch.rpm Perl interface for E-Cell Simulation Environment
perl-Bio-EUtilities-1.73-alt1.noarch.rpm Webagent which interacts with and retrieves data from NCBI's eUtils
perl-Bio-EasyYang-1-alt1.noarch.rpm A tiny interface for Bio::Tools::Run::Phylo::PAML::Yn00 module
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