Modifying splice site usage by changing the mRNP code, while maintaining the genetic code

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Documentation for package ‘ModCon’ version 1.15.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

calculateHZEIint	Calculate HZEI integral of nucleotide sequence
calculateMaxEntScanScore	Calculate MaxEntScan score of a splice site sequence
cds	CDS of firefly luciferase
changeSequenceHZEI	Adjust HZEI integral of nucleotide sequence
Codons	Table of codons and encoded amino acids
createCodonMatrix	Create codon matrix from coding nucleotide sequence
createFilialSequencePopulation	Generate new sequences by recombination
decreaseGTsiteStrength	Remove or degrade intrinsic strength of specific GT site while keeping the HZEI integral neutral.
degradeSAs	Remove or degrade intrinisc strength of splice acceptors while adjusting HZEI integral.
degradeSDs	Remove or degrade intrinisc strength of splice donors while adjusting HZEI integral.
generateRandomCodonsPerAA	Randomly choose Codon to encode amino acid sequence
getOverlappingVectorsFromVector	Create overlapping subvectors
hbg	Donor sequences and their HBS
hex	Hexamers and Z scores
increaseGTsiteStrength	Increasing intrinsic strength of specific GT site while keeping the HZEI integral neutral.
ModCon	ModCon
mutatePopulation	Randomly exchange codons within a set of sequences.
recombineTwoSequences	Generate new sequence from recombination of two sequences
selectBestAndMean	Select best HZEI and mean
selectMatingIndividuals	Selecting mating sequences from a pool of sequences
slidingWindowHZEImanipulation	Quickly manipulate HZEI integral of nucleotide sequence
startModConApp	Start GUI of VarCon.