CodonProbabilities: Codon Probabilities

Description Usage Arguments Details Value Original code in Darwin Author(s) See Also Examples

Description

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

Usage

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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)

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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. gina@cannarozzi.com

See Also

seqinr statanacoseq readstats

Examples

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

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