slidingWindowHZEImanipulation {ModCon} | R Documentation |
Quickly manipulate HZEI integral of nucleotide sequence (min. 21nt long)
slidingWindowHZEImanipulation(inSeq, increaseHZEI=TRUE)
inSeq |
Character value of nucleotide sequence (min 21nt long, only bases 'A', 'G', 'T' or 'C') |
increaseHZEI |
Logical value if HZEI integral should be increased or decreased during SD degradation. If TRUE, function aims to increase HZEI integral. |
Character value of a nucleotide sequence encoding the same amino acid sequence as inSeq
, but an increased HZEI integral, due to alternative codon selection, accomplished through sliding window optimization.
# Load R packages library('parallel') library('utils') library('data.table') # Set parameters for genetic algorithm inSeq <- 'ATGGAAGACGCCAAAAACATAAAGAAAGGCAGGCTAAGCCTAGCTTGCCATTGCCCGGCGCCATTCTATCCGCTGGAAGATGGAATT' maximizedHZEIseq <- slidingWindowHZEImanipulation(inSeq, increaseHZEI=TRUE) minimizedHZEIseq <- slidingWindowHZEImanipulation(inSeq, increaseHZEI=FALSE) #Access sequence with maximized HZEI intregral maximizedHZEIseq #Access sequence with minimized HZEI intregral minimizedHZEIseq