slidingWindowHZEImanipulation {ModCon} | R Documentation

## Quickly manipulate HZEI integral of nucleotide sequence

### Description

Quickly manipulate HZEI integral of nucleotide sequence (min. 21nt long)

### Usage

    slidingWindowHZEImanipulation(inSeq, increaseHZEI=TRUE)

### Arguments

`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.

### Value

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.

### Examples

    # 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

[Package ModCon version 1.2.0 Index]