ModCon {ModCon} | R Documentation |
Execute ModCon on a donor site within a coding sequnece either increasing or decreasing its HZEI weight.
ModCon(cds, sdSeqStartPosition, upChangeCodonsIn=16, downChangeCodonsIn=16, optimizeContext=TRUE, sdMaximalHBS=10, acMaximalMaxent=4, optiRate=100, nGenerations=50, parentSize=300, startParentSize=1000, bestRate=40, semiLuckyRate=20, luckyRate=5, mutationRate=1e-04, nCores=-1)
cds |
Character value of coding nucleotide sequence which holds the splice site of interest |
sdSeqStartPosition |
Numeric value of the position of the first nucleotide of the splice donor of interest |
upChangeCodonsIn |
Numeric value of number of codons to change upstream of the donor site of interest |
downChangeCodonsIn |
Numeric value of number of codons to change downstream of the donor site of interest |
optimizeContext |
Character value which determines, if TRUE (the default) the donor context will be adjusted to increase the splice site HEXplorer weight (SSHW), if FALSE, the SSHW will be decreased. |
sdMaximalHBS |
Numeric value of minimal HBS of SDs which should be tried to be degraded in their intrinsic strength |
acMaximalMaxent |
Numeric value of minimal MaxEntScan score of SAs which should be tried to be degraded in their intrinsic strength |
optiRate |
Numeric value setting level of HZEI integral optimization |
nGenerations |
Numeric value setting maximal number of generations |
parentSize |
Numeric value setting size of parent generations, generated from previous generations |
startParentSize |
Numeric value setting size of initiated parent generation of sequences |
bestRate |
Numeric value setting percentage how many of the fittest sequences are used to produce the next generation |
semiLuckyRate |
Numeric value setting percentage of sequences which are selected for breeding with a probability based on the respective HZEI-score integral |
luckyRate |
Numeric value setting percentage of sequences which are randomly selected for breeding |
mutationRate |
Numeric value setting chance of each codon, to mutate randomly within a child sequence |
nCores |
Numeric value setting number of cores which should be used for parallel computations. If set to '-1' all availible cores are selected. |
Creates a character value of a coding nucleotide sequence encoding the same amino acid sequence as the entered cds
, but with an alternative nucleotide surrounding around the splice donor (SD) sequence position, stated with sdSeqStartPosition
. Depending on the entered optimizeContext
, the SD surrounding is either adjusted aiming to enhance or decrease the splice site HEXplorer wheigth.
## Load R packages library('parallel') library('utils') library('data.table') ## Set parameters for simplest use of ModCon (optimizing to 100%) cds <- paste0('ATGGAAGACGCCAAAAACATAAAGAAAGGCCCGGCGCCATTCTATCCGCTGGAAGATGGAACCGCTGGAGAGCAACTGCA', 'TAAGGCTATGAAGAGATACGCCCTGGTTCCTGGAACAATTGCTTTTACAGATGCACATATCGAGGTGGACATCACTTACGCTGAGTACTTCGAAA', 'TGTCCGTTCGGTTGGCAGAAGCTATGAAACGATATGGGCTGAATACAAATCACAGAATCGTCGTATGCAGTGAAAACTCTCTTCAATTCTTTAT', 'GCCGGTGTTGGGCGCGTTATTTATCGGAGTTGCAGTTGCGCCCGCGAACGACATTTATAATGAACGTGAATTGCTCAACAGTATGGGCATTTCG', 'CAGCCTACCGTGGTGTTCGTTTCCAAAAAGGGGTTGCAAAAAATTTTGAACGTGCAAAAAAAGCTCCCAATCATCCAAAAAATTATTATCATGG', 'ATTCTAAAACGGATTACCAGGGATTTCAGTCGATGTACACGTTCGTCACATCTCATCTACCTCCCGGTTTTAATGAATACGATTTTGTGCCAGA', 'GTCCTTCGATAGGGACAAGACAATTGCACTGATCATGAACTCCTCTGGATCTACTGGTCTGCCTAAAGGTGTCGCTCTGCCTCATAGAACTGCC', 'TGCGTGAGATTCTCGCATGCCAGAGATCCTATTTTTGGCAATCAAATCATTCCGGATACTGCGATTTTAAGTGTTGTTCCATTCCATCACGGTT', 'TTGGAATGTTTACTACACTCGGATATTTGATATGTGGATTTCGAGTCGTCTTAATGTATAGATTTGAAGAAGAGCTGTTTCTGAGGAGCCTTCA', 'GGATTACAAGATTCAAAGTGCGCTGCTGGTGCCAACCCTATTCTCCTTCTTCGCCAAAAGCACTCTGATTGACAAATACGATTTATCTAATTTA', 'CACGAAATTGCTTCTGGTGGCGCTCCCCTCTCTAAGGAAGTCGGGGAAGCGGTTGCCAAGAGGTTCCATCTGCCAGGTATCAGGCAAGGATATG', 'GGCTCACTGAGACTACATCAGCTATTCTGATTACACCCGAGGGGGATGATAAACCGGGCGCGGTCGGTAAAGTTGTTCCATTTTTTGAAGCGAA', 'GGTTGTGGATCTGGATACCGGGAAAACGCTGGGCGTTAATCAAAGAGGCGAACTGTGTGTGAGAGGTCCTATGATTATGTCCGGTTATGTAAAC', 'AATCCGGAAGCGACCAACGCCTTGATTGACAAGGATGGATGGCTACATTCTGGAGACATAGCTTACTGGGACGAAGACGAACACTTCTTCATCG', 'TTGACCGCCTGAAGTCTCTGATTAAGTACAAAGGCTATCAGGTGGCTCCCGCTGAATTGGAATCCATCTTGCTCCAACACCCCAACATCTTCGA', 'CGCAGGTGTCGCAGGTCTTCCCGACGATGACGCCGGTGAACTTCCCGCCGCCGTTGTTGTTTTGGAGCACGGAAAGACGATGACGGAAAAAGAG', 'ATCGTGGATTACGTCGCCAGTCAAGTAACAACCGCGAAAAAGTTGCGCGGAGGAGTTGTGTTTGTGGACGAAGTACCGAAAGGTCTTACCGGAA', 'AACTCGACGCAAGAAAAATCAGAGAGATCCTCATAAAGGCCAAGAAGGGCGGAAAGATCGCCGTG') ## Execute ModCon finalSequence <- ModCon(cds, 1001) ## Print final cds sequence with the alternative SD nucleotide surrounding print(finalSequence) ## More parameters can be set for use of ModCon when not optimizing to 100% (e.g. 50%) ## Execute ModCon finalSequence <- ModCon(cds, 1001, upChangeCodonsIn=16, downChangeCodonsIn=16, optimizeContext=FALSE, sdMaximalHBS=10, acMaximalMaxent=4, optiRate=50, nGenerations=5, parentSize=200, startParentSize=800, bestRate=50, semiLuckyRate=10, luckyRate=5, mutationRate=1e-03, nCores=1) ## Print final cds sequence with the alternative SD nucleotide surrounding print(finalSequence)