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

## Documentation for package ‘ModCon’ version 1.0.0

- 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.