ComputeGC3syn: GC content 3rd position of synonymous codons

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

Description

ComputeGC3syn Computes the G+C content 3rd position of synonymous codons

Usage

ComputeGC3syn(tD)

Arguments

tD	Nucleotide character string

Details

Should compute the same CP as in Darwin. By definition, GC3s values are the proportion of GC nucleotides at the variable third coding position of synonymous codons. This can be used to evaluate the degree of base composition bias.

Value

o/n

Original code in Darwin

G+C content 3rd position of synonymous codons. AR (April 2007)

ComputeGC3syn:= proc(td:string)
 if member(td[-3..-1], AToCodon('$')) then d:=td[1..-4] else d:=td fi; # remove stop codon
 o := CreateArray(1..4);
 n:=0;
 for i to length(d) by 3 do
   c:=d[i..i+2];
   if length(IntToCInt(CodonToInt(c)))>1 then
     n:=n+1;
     oi:=BToInt(c[3]);
     o[oi] := o[oi]+1
   fi;
 od;
 o:=o/n;
 return(o[2]+o[3]);
end: 

Author(s)

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

See Also

seqinr statanacoseq readstats

Examples

ComputeGC3syn('ATGTGGTACTCCGACTACGGAGGATAA')

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