slidingWindowHZEImanipulation: Quickly manipulate HZEI integral of nucleotide sequence

In caggtaagtat/ModCon: Modifying splice site usage by changing the mRNP code, while maintaining the genetic code

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

caggtaagtat/ModCon documentation built on March 12, 2021, 4:12 a.m.