GeneGA (version 1.22.0)

GeneGA-package: 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.

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

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)