CodonProbabilities: Codon Probabilities

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

Description

CodonProbabilities , for Each Codon, Computes the Probability that it Occurs at Least Once in a Gene

Usage

CodonProbabilities(entries = mylist(whatout = 1))

Arguments

entries

function for importing Entries() by default

Details

Should compute the same CP as in Darwin

Value

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

Original code in Darwin

Compute CAI, the Codon Adaptation Index (Sharp and Li 1987)

CodonProbabilities := proc()
 res := CreateArray(1..64);
 for e in Entries() do
   occurs := CreateArray(1..64);
   dna := SearchTag('DNA', e);
   for c to length(dna) by 3 do
     cint := CodonToCInt(dna[c..c+2]);
     occurs[cint] := 1;
   od;
   res := res + occurs;
 od;
 res / DB[TotEntries]
end: 

Author(s)

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

See Also

seqinr statanacoseq readstats

Examples

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

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