Description Usage Arguments Value Examples
Execute ModCon on a donor site within a coding sequnece either increasing or decreasing its HZEI weight.
1 2 3 4 |
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 | ## 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)
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