GeneGA-package: Designing gene based on mRNA secondary structure and codon...

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

Description

R based Genetic algorithm for gene expression optimization considering mRNA secondary structure and codon usage bias

Details

Package:	GeneGA
Type:	Package
Version:	1.1.2
Date:	2010-11-19
License:	GPL version 2
LazyLoad:	yes

Author(s)

Zhenpeng Li, Fei Li, Xiaochen Bo and Shengqi Wang

Maintainer: Zhenpeng Li <[e-mail]>

References

Liu L.,Kang L.S.,Chen Y.P.. (1993). Non-numerical parallel algorithms(The second volume)–genetic algorithms,Science Press(In Chinese)

Tuller T, Carmi A, Vestsigian K, et al. An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation. Cell 2010, 141:344-354

See Also

GeneGA, GeneFoldGA, GeneCodon, GeneGA-class, GeneFoldGA-class, show-methods, plotGeneGA-methods, wSet

Examples

seqfile=system.file("sequence","EGFP.fasta",package="GeneGA")
seq=unlist(getSequence(read.fasta(seqfile),as.string=TRUE))
GeneGA.result=GeneFoldGA(sequence=seq,popSize=40,iters=100,crossoverRate=0.3,
         mutationChance=0.05,region=c(1,42))
plotGeneGA(GeneGA.result)
show(GeneGA.result)

GeneGA documentation built on Nov. 8, 2020, 8:17 p.m.