## ----setup, echo=FALSE, results="hide"---------------------------------------- knitr::opts_chunk$set(tidy = FALSE, cache = FALSE, dev = "png") ## ---- eval=TRUE--------------------------------------------------------------- library(ModCon) #CDS holding the respective donor site cds <- paste0('ATGGAAGACGCCAAAAACATAAAGAAAGGCCCGGCGCCATTCTATCCGCTG', 'GAAGATGGAACCGCTGGAGAGCAACTGCATAAGGCTATGAAGAGATACGCC', 'CTGGTTCCTGGAACAATTGCTTTTACAGATGCACATATCGAGGTGGACATC', 'ACTTACGCTGAGTACTTCGAA') ## Executing ModCon to increase the splice site HEXplorer weigth of ## the splice donor at position 103 cdsSSHWincreased <- ModCon(cds, 103, nCores=1) cdsSSHWincreased ## ---- eval=TRUE--------------------------------------------------------------- ## Executing ModCon to decrease the splice site HEXplorer weigth of ## the splice donor at position 103 cdsSSHWdecreased <- ModCon(cds, 103, optimizeContext=FALSE, nCores=1) cdsSSHWdecreased ## ---- eval=TRUE--------------------------------------------------------------- ## Executing ModCon to increase the splice site HEXplorer weigth of ## the splice donor at position 103 to around 60% of the maximum suppressMessages(cdsSSHWincreased <- ModCon(cds, 103, optiRate=60, nCores=1)) suppressMessages(cdsSSHWdecreased <- ModCon(cds, 103, optiRate=60, optimizeContext=FALSE, nCores=1)) cdsSSHWincreased cdsSSHWdecreased ## ---- eval=TRUE--------------------------------------------------------------- ## Executing ModCon to increase the splice site HEXplorer weigth of ## the splice donor at position 103 to around 60% of the maximum suppressMessages(cdsSSHWincreased <- ModCon(cds, 103, sdMaximalHBS=10, acMaximalMaxent=4, optiRate=60, nGenerations=5, parentSize=200, startParentSize=800, bestRate=50, semiLuckyRate=10, luckyRate=5, mutationRate=1e-03, nCores=1)) cdsSSHWincreased ## ---- eval=TRUE--------------------------------------------------------------- ## Executing ModCon to decrease the splice site HEXplorer weigth of ## the splice donor at position 103 cdsSSHWdecreased <- ModCon(cds, 103, downChangeCodonsIn=20, upChangeCodonsIn=21, nCores=1) cdsSSHWdecreased ## ---- eval=TRUE--------------------------------------------------------------- ## Decreaser HBond score of the splice donor at position 103 ## by codon selection cdsHBondDown <- decreaseGTsiteStrength(cds, 103) cdsHBondUp <- increaseGTsiteStrength(cds, 103) cdsHBondDown ## ---- eval=TRUE--------------------------------------------------------------- library(data.table) ## Initiaing the Codons matrix plus corresponding amino acids ntSequence <- 'TTTTCGATCGGGATTAGCCTCCAGGTAAGTATCTATCGATCTATGCGATAG' ## Create Codon Matrix by splitting up the sequence by 3nt fanFunc <- createCodonMatrix(ntSequence) cdsSDlow <- degradeSDs(fanFunc, maxhbs=10, increaseHZEI=TRUE) cdsSAlow <- degradeSAs(fanFunc, maxhbs=10, maxME=4, increaseHZEI=TRUE) cdsSDlow cdsSAlow ## ----sessionInfo-------------------------------------------------------------- sessionInfo()