RSCU: Relative Synonymous Codon Usage

In fredysiegrist/statanacoseq: Statistical Analyses of Codon Usage in Custom Genome Sequences

Description

RSCU Returns Relative Synonymous Codon Usage Similar tp SeqinR

Usage

RSCU(cds)

Arguments

cds	Coding sequence in reading frame

Details

Should compute the same RSCU as seqinr.

Value

Named (codons) numerical vector with relative synonymous codon usage for the 64 codons

Original code in Darwin

Relative synonymous codon usage. AR (2007)

RSCU := proc(;d:string)
  if nargs>0 then
    cc:=CodonCount(d);
  else
    cc := CodonCount();
  fi;
  rscu := CreateArray(1..64);
  for i to 64 do
    s:=0;
    syn:=IntToCInt(CIntToInt(i));
    l:=length(syn);
    for j in syn do
      s:=s+cc[j];
    od;
    if s=0 then next fi;
    rscu[i]:=cc[i]/(s/l);
  od;
  rscu;
end: 

Author(s)

Roth, A.; Siegrist, F. and Cannarozzi, G. M. [e-mail]

See Also

seqinr statanacoseq readstats

Examples

RSCU('ATGTGGTACTCCGACTACGGAGGATAA')
RSCU(c2s(mylist(whatout=1)[[1]]))

fredysiegrist/statanacoseq documentation built on May 16, 2019, 2:44 p.m.