degradeSDs {ModCon} | R Documentation |
Degrade or remove splice donor sites of certain intrinsic strength (in HBS) from a coding sequence by codon selection.
degradeSDs(fanFunc, maxhbs=10, increaseHZEI=TRUE)
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. |
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
.
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)