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#' @title SequenceAnalysis.ReverseComplement
#' @description Reverse-Complement of desired nucleotide sequence.
#' @details Reverse-Complement of desired nucleotide sequence. (atcagt -> Reverse: tgacta -> Reverse-Complement: actgat)
#' @author Babak Khorsand
#' @export SequenceAnalysis.ReverseComplement
#' @param Nucleotide_Sequence Nucleotide Sequence
#' @param UniprotKB UniProt ID of desired sequence
#' @param CDS if TRUE Reverse-Complement of CDS Region will be calculated
#' @return Reverse-Complement
#' @examples
#' SequenceAnalysis.ReverseComplement("actagtcacgatcag")
#' SequenceAnalysis.ReverseComplement(UniprotKB="O15131")
#' SequenceAnalysis.ReverseComplement(UniprotKB="O15131",CDS=TRUE)
SequenceAnalysis.ReverseComplement = function(Nucleotide_Sequence=NULL,UniprotKB=NULL,CDS=FALSE)
{
ReverseComplement=NULL
if (is.null(Nucleotide_Sequence))
{
if (is.null(UniprotKB))
{
stop("Nucleotide Sequence or UniprotKB must be set")
}else
{
Nucleotide_Sequence=SequenceAnalysis.GetNucleotideSequence(UniprotKB)
if (CDS)
{
Nucleotide_Sequence=Nucleotide_Sequence[[2]]
if (Nucleotide_Sequence=="N/A")
Nucleotide_Sequence=Nucleotide_Sequence[[3]]
}else
{
Nucleotide_Sequence=Nucleotide_Sequence[[3]]
}
}
}
if (Nucleotide_Sequence!="N/A")
{
Nucleotide_Sequence=toupper(Nucleotide_Sequence)
Nucleotide_Sequence=unlist(strsplit(Nucleotide_Sequence,""))
Nucleotide_Sequence=Nucleotide_Sequence[length(Nucleotide_Sequence):1]
a=grep("A",Nucleotide_Sequence)
t=grep("T",Nucleotide_Sequence)
c=grep("C",Nucleotide_Sequence)
g=grep("G",Nucleotide_Sequence)
Nucleotide_Sequence[a]="T"
Nucleotide_Sequence[t]="A"
Nucleotide_Sequence[c]="G"
Nucleotide_Sequence[g]="C"
ReverseComplement=paste(Nucleotide_Sequence,collapse = "")
}
if (is.null(ReverseComplement))
ReverseComplement="N/A"
names(ReverseComplement)="ReverseComplement"
return(ReverseComplement)
}
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