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GeneGA (version 1.22.0)

Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm

Description

R based Genetic algorithm for gene expression optimization by considering both mRNA secondary structure and codon usage bias, GeneGA includes the information of highly expressed genes of almost 200 genomes. Meanwhile, Vienna RNA Package is needed to ensure GeneGA to function properly.

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Version

Version

1.22.0

License

GPL version 2

Maintainer

Zhenpeng Li

Last Published

February 15th, 2017

Functions in GeneGA (1.22.0)

the function optimizes gene expression based on both mRNA secondary structure and codon usage bias

GeneFoldGA-class

Class "GeneFoldGA"

the function optimizes gene merely considering mRNA secondary structure.

Designing gene based on mRNA secondary structure and codon usage bias using Genetic algorithm, GeneGA includes the information of highly expressed genes of almost 200 genomes.

Codon Adaptation Index (CAI) w tables

plotGeneGA-methods

plotGeneGA methods of GeneGA and GeneFoldGA objects

Optimizing the codon usage of gene by replacing less usage codons with the most preference used codons or replacing the most preference used codons with less usage codons.