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#' @title Curing of biological sequences
#' @description Curates biological sequences of primer reverse.This cleaning is required for techniques such as cDNA-AFLP.
#' @param SEQs file with fasta format containing biological sequences that are to be cleaned.
#' @param PrimerR dnastring containing the reverse primer/vector sequences to be removed.
#' @return clean biological sequences and visualization of the alignments
#' @import Biostrings
#' @author Florencia I Pozzi, Silvina A. Felitti
#' @examples
#' SEQs = readDNAStringSet(system.file("sequences","SeqInputOPR.fasta", package = "CleanBSequences"))
#' PrimerR= DNAString ("GACTGCGTACCATGC")
#' DNAStringSetOPR (SEQs,PrimerR)
#' @export
DNAStringSetOPR = function (SEQs,PrimerR){
PrimerRRC = reverseComplement(PrimerR)
lengthRRC = length(PrimerRRC)
LENGTHRRC= (lengthRRC* 80)/100
lfRRC=lengthRRC-LENGTHRRC
lffRRC=as.integer(lfRRC)
ma = vmatchPattern(PrimerRRC, SEQs, max.mismatch=lffRRC)
nmatchPos2=start(ma)
A=1
B=nmatchPos2-1
C = as.integer(B)
Subseq= DNAStringSet(subseq(SEQs, start=A, end=C))
print(Subseq)
fname=tempfile()
writeXStringSet(Subseq,fname)
localAlign = pairwiseAlignment(SEQs, PrimerRRC, type = "local")
print(localAlign)
}
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