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

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.

Author
Zhenpeng Li and Haixiu Huang
Date of publication
None
Maintainer
Zhenpeng Li <zpli21@gmail.com>
License
GPL version 2
Version
1.24.0
URLs

View on Bioconductor

Man pages

GeneCodon
Optimizing the codon usage of gene by replacing less usage...
GeneFoldGA
the function optimizes gene merely considering mRNA secondary...
GeneFoldGA-class
Class "GeneFoldGA"
GeneGA
the function optimizes gene expression based on both mRNA...
GeneGA-class
Class "GeneGA"
GeneGA-package
Designing gene based on mRNA secondary structure and codon...
plotGeneGA-methods
plotGeneGA methods of GeneGA and GeneFoldGA objects
wSet
Codon Adaptation Index (CAI) w tables

Files in this package

GeneGA/.BBSoptions
GeneGA/DESCRIPTION
GeneGA/NAMESPACE
GeneGA/R
GeneGA/R/GeneCodon.R
GeneGA/R/GeneFoldGA.R
GeneGA/R/GeneGA-internal.R
GeneGA/R/GeneGA.R
GeneGA/R/GeneGA_internal.R
GeneGA/R/evaluationFunction.R
GeneGA/build
GeneGA/build/vignette.rds
GeneGA/data
GeneGA/data/wSet.rda
GeneGA/inst
GeneGA/inst/doc
GeneGA/inst/doc/GeneGA.R
GeneGA/inst/doc/GeneGA.Rnw
GeneGA/inst/doc/GeneGA.pdf
GeneGA/inst/sequence
GeneGA/inst/sequence/EGFP.fasta
GeneGA/man
GeneGA/man/GeneCodon.Rd
GeneGA/man/GeneFoldGA-class.Rd
GeneGA/man/GeneFoldGA.Rd
GeneGA/man/GeneGA-class.Rd
GeneGA/man/GeneGA-package.Rd
GeneGA/man/GeneGA.Rd
GeneGA/man/plotGeneGA-methods.Rd
GeneGA/man/wSet.Rd
GeneGA/vignettes
GeneGA/vignettes/GeneGA.Rnw
GeneGA/vignettes/GeneGA.bib