degradeSDs {ModCon} | R Documentation

## Remove or degrade intrinisc strength of splice donors while adjusting HZEI integral.

### Description

Degrade or remove splice donor sites of certain intrinsic strength (in HBS) from a coding sequence by codon selection.

### Usage

    degradeSDs(fanFunc, maxhbs=10, increaseHZEI=TRUE)

### Arguments

`fanFunc` | Codon matrix with two rows (see example below)
`maxhbs` | Numeric treshold which strength of internal donor sites should be degraded
`increaseHZEI` | Logical value of HZEI integral should be increased or decreased during SD degradation. If TRUE, function aims to increase HZEI integral.

### Value

Character value of a nucleotide sequence encoding the same amino acid as the entered codon matrix `fanFunc`, but the intrinsic strength of all present splice donors (SD) sites is degraded as much as possible, in case they exceed the given treshold `maxhbs`.

### Examples

    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)
    degradeSDs(fanFunc, maxhbs=10, increaseHZEI=TRUE)

[Package ModCon version 1.2.0 Index]